Bioconductor – Bioconductor 3.14 Released

October 27, 2021

Bioconductors:

We are pleased to announce Bioconductor 3.14, consisting of
2083 software packages, 408 experiment data packages, 904 annotation
packages, 29 workflows and 8 books.

There are 89 new software packages, 13 new data experiment packages,
10 new annotation packages, 1 new workflow, no new books, and many updates and
improvements to existing packages; Bioconductor 3.14 is compatible with R 4.1.1,
and is supported on Linux, 32- and 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. We do not currently support arm64 so arm64 Mac users who wish to install Bioconductor Mac binary packages must install the Intel 64-bit build of R available on CRAN. This release will include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews
for details and downloads.

Bioconductor used Microsoft Azure VMs during our 3.14 release process for a
critical part of our branching process for software packages. These VMs are
available to Bioconductor through our collaboration with the Microsoft Genomics
team.

Contents

To update to or install Bioconductor 3.14:

  1. Install R 4.1.1. Bioconductor 3.14 has been designed expressly for
    this version of R.

  2. Follow the instructions at
    Installing Bioconductor.

There are 89 new software packages in this release of Bioconductor.

  • atena Quantify expression of transposable
    elements (TEs) from RNA-seq data through different methods,
    including ERVmap, TEtranscripts and Telescope. A common interface
    is provided to use each of these methods, which consists of
    building a parameter object, calling the quantification function
    with this object and getting a SummarizedExperiment object as
    output container of the quantified expression profiles. The
    implementation allows one to quantify TEs and gene transcripts in
    an integrated manner.

  • benchdamic Starting from a microbiome
    dataset (16S or WMS with absolute count values) it is possible to
    perform several analysis to assess the performances of many
    differential abundance detection methods. A basic and standardized
    version of the main differential abundance analysis methods is
    supplied but the user can also add his method to the benchmark. The
    analyses focus on 4 main aspects: i) the goodness of fit of each
    method’s distributional assumptions on the observed count data, ii)
    the ability to control the false discovery rate, iii) the within
    and between method concordances, iv) the truthfulness of the
    findings if any apriori knowledge is given. Several graphical
    functions are available for result visualization.

  • BindingSiteFinder Precise knowledge
    on the binding sites of an RNA-binding protein (RBP) is key to
    understand (post-) transcriptional regulatory processes. Here we
    present a workflow that describes how exact binding sites can be
    defined from iCLIP data. The package provides functions for binding
    site definition and result visualization. For details please see
    the vignette.

  • biodbChebi The biodbChebi library provides
    access to the ChEBI Database, using biodb package framework. It
    allows to retrieve entries by their accession number. Web services
    can be accessed for searching the database by name, mass or other
    fields.

  • biodbHmdb The biodbHmdb library is an
    extension of the biodb framework package that provides access to
    the HMDB Metabolites database. It allows to download the whole HMDB
    Metabolites database locally, access entries and search for entries
    by name or description. A future version of this package will also
    include a search by mass and mass spectra annotation.

  • biodbKegg The biodbKegg library is an
    extension of the biodb framework package that provides access to
    the KEGG databases Compound, Enzyme, Genes, Module, Orthology and
    Reaction. It allows to retrieve entries by their accession numbers.
    Web services like “find”, “list” and “findExactMass” are also
    available. Some functions for navigating along the pathways have
    also been implemented.

  • biodbLipidmaps The biodbLipidmaps
    library provides access to the Lipidmaps Structure Database, using
    biodb package framework. It allows to retrieve entries by their
    accession number, and run web the services lmsdSearch and
    lmsdRecord.

  • biodbUniprot The biodbUniprot library is
    an extension of the biodb framework package. It provides access to
    the UniProt database. It allows to retrieve entries by their
    accession number, and run web service queries for searching for
    entries.

  • BioPlex The BioPlex package implements access
    to the BioPlex protein-protein interaction networks and related
    resources from within R. Besides protein-protein interaction
    networks for HEK293 and HCT116 cells, this includes access to CORUM
    protein complex data, and transcriptome and proteome data for the
    two cell lines. Functionality focuses on importing the various data
    resources and storing them in dedicated Bioconductor data
    structures, as a foundation for integrative downstream analysis of
    the data.

  • bugsigdbr The bugsigdbr package implements
    convenient access to bugsigdb.org from within R/Bioconductor. The
    goal of the package is to facilitate import of BugSigDB data into
    R/Bioconductor, provide utilities for extracting microbe
    signatures, and enable export of the extracted signatures to plain
    text files in standard file formats such as GMT.

  • BUSseq BUSseq R package fits an interpretable
    Bayesian hierarchical model—the Batch Effects Correction with
    Unknown Subtypes for scRNA seq Data (BUSseq)—to correct batch
    effects in the presence of unknown cell types. BUSseq is able to
    simultaneously correct batch effects, clusters cell types, and
    takes care of the count data nature, the overdispersion, the
    dropout events, and the cell-specific sequencing depth of scRNA-seq
    data. After correcting the batch effects with BUSseq, the corrected
    value can be used for downstream analysis as if all cells were
    sequenced in a single batch. BUSseq can integrate read count
    matrices obtained from different scRNA-seq platforms and allow cell
    types to be measured in some but not all of the batches as long as
    the experimental design fulfills the conditions listed in our
    manuscript.

  • cageminer This package aims to integrate
    GWAS-derived SNPs and coexpression networks to mine candidate genes
    associated with a particular phenotype. For that, users must define
    a set of guide genes, which are known genes involved in the studied
    phenotype. Additionally, the mined candidates can be given a score
    that favor candidates that are hubs and/or transcription factors.
    The scores can then be used to rank and select the top n most
    promising genes for downstream experiments.

  • CellBarcode This package performs Cellular
    DNA Barcode (genetic lineage tracing) analysis. The package can
    handle all kinds of DNA barcodes, as long as the barcode within a
    single sequencing read and has a pattern which can be matched by a
    regular expression. This package can handle barcode with flexible
    length, with or without UMI (unique molecular identifier). This
    tool also can be used for pre-processing of some amplicon data such
    as CRISPR gRNA screening, immune repertoire sequencing and meta
    genome data.

  • Cepo Defining the identity of a cell is
    fundamental to understand the heterogeneity of cells to various
    environmental signals and perturbations. We present Cepo, a new
    method to explore cell identities from single-cell RNA-sequencing
    data using differential stability as a new metric to define cell
    identity genes. Cepo computes cell-type specific gene statistics
    pertaining to differential stable gene expression.

  • cfDNAPro cfDNA fragment size metrics are
    important features for utilizing liquid biopsy in tumor early
    detection, diagnosis, therapy personlization and monitoring.
    Analyzing and visualizing insert size metrics could be time
    intensive. This package intends to simplify this exploration
    process, and it offers two sets of functions for data
    characterization and data visualization.

  • cliProfiler An easy and fast way to
    visualize and profile the high-throughput IP data. This package
    generates the meta gene profile and other profiles. These profiles
    could provide valuable information for understanding the IP
    experiment results.

  • Cogito Biological studies often consist of
    multiple conditions which are examined with different laboratory
    set ups like RNA-sequencing or ChIP-sequencing. To get an overview
    about the whole resulting data set, Cogito provides an automated,
    complete, reproducible and clear report about all samples and basic
    comparisons between all different samples. This report can be used
    as documentation about the data set or as starting point for
    further custom analysis.

  • csdR This package contains functionality to run
    differential gene co-expression across two different conditions.
    The algorithm is inspired by Voigt et al. 2017 and finds Conserved,
    Specific and Differentiated genes (hence the name CSD). This
    package include efficient and variance calculation by bootstrapping
    and Welford’s algorithm.

  • CyTOFpower This package is a tool to
    predict the power of CyTOF experiments in the context of
    differential state analyses. The package provides a shiny app with
    two options to predict the power of an experiment: i. generation of
    in-sicilico CyTOF data, using users input ii. browsing in a grid of
    parameters for which the power was already precomputed.

  • cytoKernel cytoKernel implements a
    kernel-based score test to identify differentially expressed
    features in high-dimensional biological experiments. This approach
    can be applied across many different high-dimensional biological
    data including gene expression data and dimensionally reduced
    cytometry-based marker expression data. In this R package, we
    implement functions that compute the feature-wise p values and
    their corresponding adjusted p values. Additionally, it also
    computes the feature-wise shrunk effect sizes and their
    corresponding shrunken effect size. Further, it calculates the
    percent of differentially expressed features and plots
    user-friendly heatmap of the top differentially expressed features
    on the rows and samples on the columns.

  • deconvR This package provides a collection of
    functions designed for analyzing deconvolution of the bulk
    sample(s) using an atlas of reference omic signature profiles and a
    user-selected model. Users are given the option to create or extend
    a reference atlas and,also simulate the desired size of the bulk
    signature profile of the reference cell types.The package includes
    the cell-type-specific methylation atlas and, Illumina Epic B5
    probe ids that can be used in deconvolution. Additionally,we
    included BSmeth2Probe, to make mapping WGBS data to their probe IDs
    easier.

  • DelayedTensor DelayedTensor operates
    Tensor arithmetic directly on DelayedArray object. DelayedTensor
    provides some generic function related to Tensor
    arithmetic/decompotision and dispatches it on the DelayedArray
    class. DelayedTensor also suppors Tensor contraction by einsum
    function, which is inspired by numpy einsum.

  • Dino Dino normalizes single-cell, mRNA sequencing
    data to correct for technical variation, particularly sequencing
    depth, prior to downstream analysis. The approach produces a matrix
    of corrected expression for which the dependency between sequencing
    depth and the full distribution of normalized expression; many
    existing methods aim to remove only the dependency between
    sequencing depth and the mean of the normalized expression. This is
    particuarly useful in the context of highly sparse datasets such as
    those produced by 10X genomics and other uninque molecular
    identifier (UMI) based microfluidics protocols for which the
    depth-dependent proportion of zeros in the raw expression data can
    otherwise present a challenge.

  • dStruct dStruct identifies differentially
    reactive regions from RNA structurome profiling data. dStruct is
    compatible with a broad range of structurome profiling
    technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq,
    SHAPE-Seq, etc. See Choudhary et al, Genome Biology, 2019 for the
    underlying method.

  • easier This package provides a workflow for the
    use of EaSIeR tool, developed to assess patients’ likelihood to
    respond to ICB therapies providing just the patients’ RNA-seq data
    as input. We integrate RNA-seq data with different types of prior
    knowledge to extract quantitative descriptors of the tumor
    microenvironment from several points of view, including composition
    of the immune repertoire, and activity of intra- and extra-cellular
    communications. Then, we use multi-task machine learning trained in
    TCGA data to identify how these descriptors can simultaneously
    predict several state-of-the-art hallmarks of anti-cancer immune
    response. In this way we derive cancer-specific models and identify
    cancer-specific systems biomarkers of immune response. These
    biomarkers have been experimentally validated in the literature and
    the performance of EaSIeR predictions has been validated using
    independent datasets form four different cancer types with patients
    treated with anti-PD1 or anti-PDL1 therapy.

  • enhancerHomologSearch Get ENCODE
    data of enhancer region via H3K4me1 peaks and search homolog
    regions for given sequences. The candidates of enhancer homolog
    regions can be filtered by distance to target TSS. The top
    candidates from human and mouse will be aligned to each other and
    then exported as multiple alignments with given enhancer.

  • epistack The epistack package main objective
    is the visualizations of stacks of genomic tracks (such as, but not
    restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic
    conservation data) centered at genomic regions of interest.

  • FindIT2 This package implements functions to
    find influential TF and target based on different input type. It
    have five module: Multi-peak multi-gene annotaion(mmPeakAnno
    module), Calculate regulation potential(calcRP module), Find
    influential Target based on ChIP-Seq and RNA-Seq data(Find
    influential Target module), Find influential TF based on different
    input(Find influential TF module), Calculate peak-gene or peak-peak
    correlation(peakGeneCor module). And there are also some other
    useful function like integrate different source information,
    calculate jaccard similarity for your TF.

  • FLAMES Semi-supervised isoform detection and
    annotation from both bulk and single-cell long read RNA-seq data.
    Flames provides automated pipelines for analysing isoforms, as well
    as intermediate functions for manual execution.

  • genomicInstability This package
    contain functions to run genomic instability analysis (GIA) from
    scRNA-Seq data. GIA estimates the association between gene
    expression and genomic location of the coding genes. It uses the
    aREA algorithm to quantify the enrichment of sets of contiguous
    genes (loci-blocks) on the gene expression profiles and estimates
    the Genomic Instability Score (GIS) for each analyzed cell.

  • GeoDiff A series of statistical models using
    count generating distributions for background modelling, feature
    and sample QC, normalization and differential expression analysis
    on GeoMx RNA data. The application of these methods are
    demonstrated by example data analysis vignette.

  • GEOexplorer GEOexplorer is a Shiny app
    that enables exploratory data analysis and differential gene
    expression of gene expression analysis on microarray gene
    expression datasets held on the GEO database. The outputs are
    interactive graphs that enable users to explore the results of the
    analysis. The development of GEOexplorer was made possible because
    of the excellent code provided by GEO2R (https:
    //www.ncbi.nlm.nih.gov/geo/geo2r/).

  • ggmsa A visual exploration tool for multiple
    sequence alignment and associated data. Supports MSA of DNA, RNA,
    and protein sequences using ‘ggplot2’. Multiple sequence alignment
    can easily be combined with other ‘ggplot2’ plots, such as
    phylogenetic tree Visualized by ‘ggtree’, boxplot, genome map and
    so on. More features: visualization of sequence logos, sequence
    bundles, RNA secondary structures and detection of sequence
    recombinations.

  • ggspavis Visualization functions for
    spatially resolved transcriptomics datasets stored in
    SpatialExperiment format. Includes functions to create several
    types of plots for data from from spot-based (e.g. 10x Genomics
    Visium) and molecule-based (e.g. seqFISH) technological platforms.

  • HPiP HPiP (Host-Pathogen Interaction Prediction)
    uses an ensemble learning algorithm for prediction of host-pathogen
    protein-protein interactions (HP-PPIs) using structural and
    physicochemical descriptors computed from amino acid-composition of
    host and pathogen proteins.The proposed package can effectively
    address data shortages and data unavailability for HP-PPI network
    reconstructions. Moreover, establishing computational frameworks in
    that regard will reveal mechanistic insights into infectious
    diseases and suggest potential HP-PPI targets, thus narrowing down
    the range of possible candidates for subsequent wet-lab
    experimental validations.

  • imcRtools This R package supports the
    handling and analysis of imaging mass cytometry and other highly
    multiplexed imaging data. The main functionality includes reading
    in single-cell data after image segmentation and measurement, data
    formatting to perform channel spillover correction and a number of
    spatial analysis approaches. First, cell-cell interactions are
    detected via spatial graph construction; these graphs can be
    visualized with cells representing nodes and interactions
    representing edges. Furthermore, per cell, its direct neighbours
    are summarized to allow spatial clustering. Per image/grouping
    level, interactions between types of cells are counted, averaged
    and compared against random permutations. In that way, types of
    cells that interact more (attraction) or less (avoidance)
    frequently than expected by chance are detected.

  • iPath iPath is the Bioconductor package used for
    calculating personalized pathway score and test the association
    with survival outcomes. Abundant single-gene biomarkers have been
    identified and used in the clinics. However, hundreds of oncogenes
    or tumor-suppressor genes are involved during the process of
    tumorigenesis. We believe individual-level expression patterns of
    pre-defined pathways or gene sets are better biomarkers than single
    genes. In this study, we devised a computational method named iPath
    to identify prognostic biomarker pathways, one sample at a time. To
    test its utility, we conducted a pan-cancer analysis across 14
    cancer types from The Cancer Genome Atlas and demonstrated that
    iPath is capable of identifying highly predictive biomarkers for
    clinical outcomes, including overall survival, tumor subtypes, and
    tumor stage classifications. We found that pathway-based biomarkers
    are more robust and effective than single genes.

  • m6Aboost This package can help user to run
    the m6Aboost model on their own miCLIP2 data. The package includes
    functions to assign the read counts and get the features to run the
    m6Aboost model. The miCLIP2 data should be stored in a GRanges
    object. More details can be found in the vignette.

  • MAI A two-step approach to imputing missing data
    in metabolomics. Step 1 uses a random forest classifier to classify
    missing values as either Missing Completely at Random/Missing At
    Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are
    combined because it is often difficult to distinguish these two
    missing types in metabolomics data. Step 2 imputes the missing
    values based on the classified missing mechanisms, using the
    appropriate imputation algorithms. Imputation algorithms tested and
    available for MCAR/MAR include Bayesian Principal Component
    Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors
    (Multi_nsKNN), and Random Forest. Imputation algorithms tested and
    available for MNAR include nsKNN and a single imputation approach
    for imputation of metabolites where left-censoring is present.

  • metapone The package conducts pathway testing
    from untargetted metabolomics data. It requires the user to supply
    feature-level test results, from case-control testing, regression,
    or other suitable feature-level tests for the study design. Weights
    are given to metabolic features based on how many metabolites they
    could potentially match to. The package can combine positive and
    negative mode results in pathway tests.

  • methylclock This package allows to
    estimate chronological and gestational DNA methylation (DNAm) age
    as well as biological age using different methylation clocks.
    Chronological DNAm age (in years) : Horvath’s clock, Hannum’s
    clock, BNN, Horvath’s skin+blood clock, PedBE clock and Wu’s clock.
    Gestational DNAm age : Knight’s clock, Bohlin’s clock, Mayne’s
    clock and Lee’s clocks. Biological DNAm clocks : Levine’s clock and
    Telomere Length’s clock.

  • miaSim Microbiome time series simulation with
    generalized Lotka-Volterra model, Self-Organized Instability (SOI),
    and other models. Hubbell’s Neutral model is used to determine the
    abundance matrix. The resulting abundance matrix is applied to
    SummarizedExperiment or TreeSummarizedExperiment objects.

  • microbiomeMarker To date, a number of
    methods have been developed for microbiome marker discovery based
    on metagenomic profiles, e.g. LEfSe. However, all of these methods
    have its own advantages and disadvantages, and none of them is
    considered standard or universal. Moreover, different programs or
    softwares may be development using different programming languages,
    even in different operating systems. Here, we have developed an
    all-in-one R package microbiomeMarker that integrates commonly used
    differential analysis methods as well as three machine
    learning-based approaches, including Logistic regression, Random
    forest, and Support vector machine, to facilitate the
    identification of microbiome markers.

  • MicrobiomeProfiler This is an
    R/shiny package to perform functional enrichment analysis for
    microbiome data. This package was based on clusterProfiler.
    Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG
    enrichment analysis, Microbe-Disease association enrichment
    analysis, Metabo-Pathway analysis.

  • mitoClone2 This package primarily
    identifies variants in mitochondrial genomes from BAM alignment
    files. It filters these variants to remove RNA editing events then
    estimates their evolutionary relationship (i.e. their phylogenetic
    tree) and groups single cells into clones. It also visualizes the
    mutations and providing additional genomic context.

  • monaLisa Useful functions to work with
    sequence motifs in the analysis of genomics data. These include
    methods to annotate genomic regions or sequences with predicted
    motif hits and to identify motifs that drive observed changes in
    accessibility or expression. Functions to produce informative
    visualizations of the obtained results are also provided.

  • mosbi This package is a implementation of
    biclustering ensemble method MoSBi (Molecular signature
    Identification from Biclustering). MoSBi provides standardized
    interfaces for biclustering results and can combine their results
    with a multi-algorithm ensemble approach to compute robust ensemble
    biclusters on molecular omics data. This is done by computing
    similarity networks of biclusters and filtering for overlaps using
    a custom error model. After that, the louvain modularity it used to
    extract bicluster communities from the similarity network, which
    can then be converted to ensemble biclusters. Additionally, MoSBi
    includes several network visualization methods to give an intuitive
    and scalable overview of the results. MoSBi comes with several
    biclustering algorithms, but can be easily extended to new
    biclustering algorithms.

  • MsBackendRawFileReader
    implements a MsBackend for the Spectra package using Thermo Fisher
    Scientific’s NewRawFileReader .Net libraries. The package is
    generalizing the functionality introduced by the rawrr package
    (Kockmann T. et al. (2020) <doi:10.1101/2020.10.30.362533>) Methods
    defined in this package are supposed to extend the Spectra
    Bioconductor package.

  • MSstatsLiP Tools for LiP peptide and
    protein significance analysis. Provides functions for
    summarization, estimation of LiP peptide abundance, and detection
    of changes across conditions. Utilizes functionality across the
    MSstats family of packages.

  • NanoTube NanoTube includes functions for the
    processing, quality control, analysis, and visualization of
    NanoString nCounter data. Analysis functions include differential
    analysis and gene set analysis methods, as well as postprocessing
    steps to help understand the results. Additional functions are
    included to enable interoperability with other Bioconductor
    NanoString data analysis packages.

  • netOmics netOmics is a multi-omics networks
    builder and explorer. It uses a combination of network inference
    algorithms and and knowledge-based graphs to build multi-layered
    networks. The package can be combined with timeOmics to incorporate
    time-course expression data and build sub-networks from multi-omics
    kinetic clusters. Finally, from the generated multi-omics networks,
    propagation analyses allow the identification of missing biological
    functions (1), multi-omics mechanisms (2) and molecules between
    kinetic clusters (3). This helps to resolve complex regulatory
    mechanisms.

  • NeuCA NeuCA is is a neural-network based method
    for scRNA-seq data annotation. It can automatically adjust its
    classification strategy depending on cell type correlations, to
    accurately annotate cell. NeuCA can automatically utilize the
    structure information of the cell types through a hierarchical tree
    to improve the annotation accuracy. It is especially helpful when
    the data contain closely correlated cell types.

  • nullranges Modular package for generation
    of sets of ranges representing the null hypothesis. These can take
    the form of bootstrap samples of ranges (using the block bootstrap
    framework of Bickel et al 2010), or sets of control ranges that are
    matched across one or more covariates. nullranges is designed to be
    inter-operable with other packages for analysis of genomic overlap
    enrichment, including the plyranges Bioconductor package.

  • NxtIRFcore Interactively analyses Intron
    Retention and Alternative Splicing Events (ASE) in RNA-seq data.
    NxtIRF quantifies ASE events in BAM files aligned to the genome
    using a splice-aware aligner such as STAR. The core quantitation
    algorithm relies on the IRFinder/C++ engine ported via Rcpp for
    multi-platform compatibility. In addition, NxtIRF provides
    convenient pipelines for downstream analysis and publication-ready
    visualisation tools.

  • ODER The aim of ODER is to identify previously
    unannotated expressed regions (ERs) using RNA-sequencing data. For
    this purpose, ODER defines and optimises the definition of ERs,
    then connected these ERs to genes using junction data. In this way,
    ODER improves gene annotation. Gene annotation is a staple input of
    many bioinformatic pipelines and a more complete gene annotation
    can enable more accurate interpretation of disease associated
    variants.

  • orthogene orthogene is an R package for easy
    mapping of orthologous genes across hundreds of species. It pulls
    up-to-date interspecies gene ortholog mappings across 700+
    organisms. It also provides various utility functions to map common
    objects (e.g. data.frames, gene expression matrices, lists) onto
    1:1 gene orthologs from any other species.

  • pairkat PaIRKAT is model framework for
    assessing statistical relationships between networks of metabolites
    (pathways) and an outcome of interest (phenotype). PaIRKAT queries
    the KEGG database to determine interactions between metabolites
    from which network connectivity is constructed. This model
    framework improves testing power on high dimensional data by
    including graph topography in the kernel machine regression
    setting. Studies on high dimensional data can struggle to include
    the complex relationships between variables. The semi-parametric
    kernel machine regression model is a powerful tool for capturing
    these types of relationships. They provide a framework for testing
    for relationships between outcomes of interest and high dimensional
    data such as metabolomic, genomic, or proteomic pathways. PaIRKAT
    uses known biological connections between high dimensional
    variables by representing them as edges of ‘graphs’ or ‘networks.’
    It is common for nodes (e.g. metabolites) to be disconnected from
    all others within the graph, which leads to meaningful decreases in
    testing power whether or not the graph information is included. We
    include a graph regularization or ‘smoothing’ approach for managing
    this issue.

  • pengls Combine generalised least squares
    methodology from the nlme package for dealing with autocorrelation
    with penalised least squares methods from the glmnet package to
    deal with high dimensionality. This pengls packages glues them
    together through an iterative loop. The resulting method is
    applicable to high dimensional datasets that exhibit
    autocorrelation, such as spatial or temporal data.

  • plotgardener Coordinate-based genomic
    visualization package for R. It grants users the ability to
    programmatically produce complex, multi-paneled figures. Tailored
    for genomics, plotgardener allows users to visualize large complex
    genomic datasets and provides exquisite control over how plots are
    placed and arranged on a page.

  • ProteoDisco ProteoDisco is an R package to
    facilitate proteogenomics studies. It houses functions to create
    customized (mutant) protein databases based on user-submitted
    genomic variants, splice-junctions, fusion genes and manual
    transcript sequences. The flexible workflow can be adopted to suit
    a myriad of research and experimental settings.

  • rGenomeTracks rGenomeTracks package
    leverages the power of pyGenomeTracks software with the
    interactivity of R. pyGenomeTracks is a python software that offers
    robust method for visualizing epigenetic data files like
    narrowPeak, Hic matrix, TADs and arcs, however though, here is no
    way currently to use it within R interactive session. rGenomeTracks
    wrapped the whole functionality of pyGenomeTracks with additional
    utilites to make to more pleasant for R users.

  • RiboCrypt R Package for interactive
    visualization and browsing NGS data. It contains a browser for both
    transcript and genomic coordinate view. In addition a QC and
    general metaplots are included, among others differential
    translation plots and gene expression plots. The package is still
    under development.

  • RLSeq RLSeq is a toolkit for analyzing and
    evaluating R-loop mapping datasets. RLSeq serves two primary
    purposes:
    (1) to facilitate the evaluation of dataset quality
    (2) to enable R-loop analysis in the context of publicly-available
    data sets from RLBase. The package is intended to provide a simple
    pipeline, called with the RLSeq() function, which performs all
    main analyses. Individual functions are also accessible and provide
    custom analysis capabilities. Finally an HTML report is generated
    with report().

  • rmspc The rmspc package runs MSPC (Multiple
    Sample Peak Calling) software using R. The analysis of ChIP-seq
    samples outputs a number of enriched regions (commonly known as
    “peaks”), each indicating a protein-DNA interaction or a specific
    chromatin modification. When replicate samples are analyzed,
    overlapping peaks are expected. This repeated evidence can
    therefore be used to locally lower the minimum significance
    required to accept a peak. MSPC uses combined evidence from
    replicated experiments to evaluate peak calling output, rescuing
    peaks, and reduce false positives. It takes any number of
    replicates as input and improves sensitivity and specificity of
    peak calling on each, and identifies consensus regions between the
    input samples.

  • scanMiR A set of tools for working with miRNA
    affinity models (KdModels), efficiently scanning for miRNA binding
    sites, and predicting target repression. It supports scanning using
    miRNA seeds, full miRNA sequences (enabling 3’ alignment) and
    KdModels, and includes the prediction of slicing and TDMD sites.
    Finally, it includes utility and plotting functions (e.g. for the
    visual representation of miRNA-target alignment).

  • scanMiRApp A shiny interface to the scanMiR
    package. The application enables the scanning of transcripts and
    custom sequences for miRNA binding sites, the visualization of
    KdModels and binding results, as well as browsing predicted
    repression data. In addition contains the IndexedFst class for fast
    indexed reading of large GenomicRanges or data.frames, and some
    utilities for facilitating scans and identifying enriched
    miRNA-target pairs.

  • scAnnotatR The package comprises a set of
    pretrained machine learning models to predict basic immune cell
    types. This enables all users to quickly get a first annotation of
    the cell types present in their dataset without requiring prior
    knowledge. scAnnotatR also allows users to train their own models
    to predict new cell types based on specific research needs.

  • scatterHatch The objective of this
    package is to efficiently create scatterplots where groups can be
    distinguished by color and texture. Visualizations in computational
    biology tend to have many groups making it difficult to distinguish
    between groups solely on color. Thus, this package is useful for
    increasing the accessibility of scatterplot visualizations to those
    with visual impairments such as color blindness.

  • scReClassify A post hoc cell type
    classification tool to fine-tune cell type annotations generated by
    any cell type classification procedure with semi-supervised
    learning algorithm AdaSampling technique. The current version of
    scReClassify supports Support Vector Machine and Random Forest as a
    base classifier.

  • scShapes We present a novel statistical
    framework for identifying differential distributions in single-cell
    RNA-sequencing (scRNA-seq) data between treatment conditions by
    modeling gene expression read counts using generalized linear
    models (GLMs). We model each gene independently under each
    treatment condition using error distributions Poisson (P), Negative
    Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated
    Negative Binomial (ZINB) with log link function and model based
    normalization for differences in sequencing depth. Since all four
    distributions considered in our framework belong to the same family
    of distributions, we first perform a Kolmogorov-Smirnov (KS) test
    to select genes belonging to the family of ZINB distributions.
    Genes passing the KS test will be then modeled using GLMs. Model
    selection is done by calculating the Bayesian Information Criterion
    (BIC) and likelihood ratio test (LRT) statistic.

  • scTreeViz scTreeViz provides classes to
    support interactive data aggregation and visualization of single
    cell RNA-seq datasets with hierarchies for e.g. cell clusters at
    different resolutions. The TreeIndex class provides methods to
    manage hierarchy and split the tree at a given resolution or across
    resolutions. The TreeViz class extends SummarizedExperiment and
    can performs quick aggregations on the count matrix defined by
    clusters.

  • segmenter Chromatin segmentation analysis
    transforms ChIP-seq data into signals over the genome. The latter
    represents the observed states in a multivariate Markov model to
    predict the chromatin’s underlying states. ChromHMM, written in
    Java, integrates histone modification datasets to learn the
    chromatin states de-novo. The goal of this package is to call
    chromHMM from within R, capture the output files in an S4 object
    and interface to other relevant Bioconductor analysis tools. In
    addition, segmenter provides functions to test, select and
    visualize the output of the segmentation.

  • sparrow Provides a unified interface to a
    variety of GSEA techniques from different bioconductor packages.
    Results are harmonized into a single object and can be interrogated
    uniformly for quick exploration and interpretation of results.
    Interactive exploration of GSEA results is enabled through a shiny
    app provided by a sparrow.shiny sibling package.

  • spatialDE SpatialDE is a method to find
    spatially variable genes (SVG) from spatial transcriptomics data.
    This package provides wrappers to use the Python SpatialDE library
    in R, using reticulate and basilisk.

  • spatzie Identifies motifs that are
    significantly co-enriched from enhancer-promoter interaction data.
    While enhancer-promoter annotation is commonly used to define
    groups of interaction anchors, spatzie also supports co-enrichment
    analysis between preprocessed interaction anchors. Supports BEDPE
    interaction data derived from genome-wide assays such as HiC,
    ChIA-PET, and HiChIP. Can also be used to look for differentially
    enriched motif pairs between two interaction experiments.

  • spiky spiky implements methods and model
    generation for cfMeDIP (cell-free methylated DNA
    immunoprecipitation) with spike-in controls. CfMeDIP is an
    enrichment protocol which avoids destructive conversion of scarce
    template, making it ideal as a “liquid biopsy,” but creating
    certain challenges in comparing results across specimens, subjects,
    and experiments. The use of synthetic spike-in standard oligos
    allows diagnostics performed with cfMeDIP to quantitatively compare
    samples across subjects, experiments, and time points in both
    relative and absolute terms.

  • surfaltr Cell surface proteins form a major
    fraction of the druggable proteome and can be used for
    tissue-specific delivery of oligonucleotide/cell-based
    therapeutics. Alternatively spliced surface protein isoforms have
    been shown to differ in their subcellular localization and/or their
    transmembrane (TM) topology. Surface proteins are hydrophobic and
    remain difficult to study thereby necessitating the use of TM
    topology prediction methods such as TMHMM and Phobius. However,
    there exists a need for bioinformatic approaches to streamline
    batch processing of isoforms for comparing and visualizing
    topologies. To address this gap, we have developed an R package,
    surfaltr. It pairs inputted isoforms, either known alternatively
    spliced or novel, with their APPRIS annotated principal
    counterparts, predicts their TM topologies using TMHMM or Phobius,
    and generates a customizable graphical output. Further, surfaltr
    facilitates the prioritization of biologically diverse isoform
    pairs through the incorporation of three different ranking metrics
    and through protein alignment functions. Citations for programs
    mentioned here can be found in the vignette.

  • svaNUMT svaNUMT contains functions for
    detecting NUMT events from structural variant calls. It takes
    structural variant calls in GRanges of breakend notation and
    identifies NUMTs by nuclear-mitochondrial breakend junctions. The
    main function reports candidate NUMTs if there is a pair of valid
    insertion sites found on the nuclear genome within a certain
    distance threshold. The candidate NUMTs are reported by events.

  • svaRetro svaRetro contains functions for
    detecting retrotransposed transcripts (RTs) from structural variant
    calls. It takes structural variant calls in GRanges of breakend
    notation and identifies RTs by exon-exon junctions and insertion
    sites. The candidate RTs are reported by events and annotated with
    information of the inserted transcripts.

  • synapsis Synapsis is a Bioconductor software
    package for automated (unbiased and reproducible) analysis of
    meiotic immunofluorescence datasets. The primary functions of the
    software can
    i) identify cells in meiotic prophase that are
    labelled by a synaptonemal complex axis or central element protein,
    ii) isolate individual synaptonemal complexes and measure their
    physical length,
    iii) quantify foci and co-localise them with
    synaptonemal complexes,
    iv) measure interference between
    synaptonemal complex-associated foci. The software has applications
    that extend to multiple species and to the analysis of other
    proteins that label meiotic prophase chromosomes. The software
    converts meiotic immunofluorescence images into R data frames that
    are compatible with machine learning methods. Given a set of
    microscopy images of meiotic spread slides, synapsis crops images
    around individual single cells, counts colocalising foci on strands
    on a per cell basis, and measures the distance between foci on any
    given strand.

  • tanggle Offers functions for plotting split
    (or implicit) networks (unrooted, undirected) and explicit networks
    (rooted, directed) with reticulations extending. ‘ggtree’ and using
    functions from ‘ape’ and ‘phangorn’. It extends the ‘ggtree’
    package [@Yu2017] to allow the visualization of phylogenetic
    networks using the ‘ggplot2’ syntax. It offers an alternative to
    the plot functions already available in ‘ape’ Paradis and Schliep
    (2019) <doi:10.1093/bioinformatics/bty633> and ‘phangorn’ Schliep
    (2011) <doi:10.1093/bioinformatics/btq706>.

  • TargetDecoy A first step in the data
    analysis of Mass Spectrometry (MS) based proteomics data is to
    identify peptides and proteins. With this respect the huge number
    of experimental mass spectra typically have to be assigned to
    theoretical peptides derived from a sequence database. Search
    engines are used for this purpose. These tools compare each of the
    observed spectra to all candidate theoretical spectra derived from
    the sequence data base and calculate a score for each comparison.
    The observed spectrum is then assigned to the theoretical peptide
    with the best score, which is also referred to as the peptide to
    spectrum match (PSM). It is of course crucial for the downstream
    analysis to evaluate the quality of these matches. Therefore False
    Discovery Rate (FDR) control is used to return a reliable list
    PSMs. The FDR, however, requires a good characterisation of the
    score distribution of PSMs that are matched to the wrong peptide
    (bad target hits). In proteomics, the target decoy approach (TDA)
    is typically used for this purpose. The TDA method matches the
    spectra to a database of real (targets) and nonsense peptides
    (decoys). A popular approach to generate these decoys is to reverse
    the target database. Hence, all the PSMs that match to a decoy are
    known to be bad hits and the distribution of their scores are used
    to estimate the distribution of the bad scoring target PSMs. A
    crucial assumption of the TDA is that the decoy PSM hits have
    similar properties as bad target hits so that the decoy PSM scores
    are a good simulation of the target PSM scores. Users, however,
    typically do not evaluate these assumptions. To this end we
    developed TargetDecoy to generate diagnostic plots to evaluate the
    quality of the target decoy method.

  • transformGamPoi Variance-stabilizing
    transformations help with the analysis of heteroskedastic data
    (i.e., data where the variance is not constant, like count data).
    This package provide two types of variance stabilizing
    transformations: (1) methods based on the delta method (e.g.,
    ‘acosh’, ‘log(x+1)’), (2) model residual based (Pearson and
    randomized quantile residuals).

  • traviz traviz provides a suite of functions to
    plot trajectory related objects from Bioconductor packages. It
    allows plotting trajectories in reduced dimension, as well as
    averge gene expression smoothers as a function of pseudotime.
    Asides from general utility functions, traviz also allows plotting
    trajectories estimated by Slingshot, as well as smoothers estimated
    by tradeSeq. Furthermore, it allows for visualization of Slingshot
    trajectories using ggplot2.

  • TRESS This package is devoted to analyzing
    MeRIP-seq data. Current functionality is for detection of
    transcriptome-wide m6A methylation regions. The method is based on
    hierarchical negative binomial models.

  • tripr TRIP is a software framework that provides
    analytics services on antigen receptor (B cell receptor
    immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data.
    It is a web application written in R Shiny. It takes as input the
    output files of the IMGT/HighV-Quest tool. Users can select to
    analyze the data from each of the input samples separately, or the
    combined data files from all samples and visualize the results
    accordingly.

  • txcutr Various mRNA sequencing library
    preparation methods generate sequencing reads specifically from the
    transcript ends. Analyses that focus on quantification of isoform
    usage from such data can be aided by using truncated versions of
    transcriptome annotations, both at the alignment or
    pseudo-alignment stage, as well as in downstream analysis. This
    package implements some convenience methods for readily generating
    such truncated annotations and their corresponding sequences.

  • VAExprs A fundamental problem in biomedical
    research is the low number of observations, mostly due to a lack of
    available biosamples, prohibitive costs, or ethical reasons. By
    augmenting a few real observations with artificially generated
    samples, their analysis could lead to more robust and higher
    reproducible. One possible solution to the problem is the use of
    generative models, which are statistical models of data that
    attempt to capture the entire probability distribution from the
    observations. Using the variational autoencoder (VAE), a well-known
    deep generative model, this package is aimed to generate samples
    with gene expression data, especially for single-cell RNA-seq data.
    Furthermore, the VAE can use conditioning to produce specific cell
    types or subpopulations. The conditional VAE (CVAE) allows us to
    create targeted samples rather than completely random ones.

  • veloviz VeloViz uses each cell’s current
    observed and predicted future transcriptional states inferred from
    RNA velocity analysis to build a nearest neighbor graph between
    cells in the population. Edges are then pruned based on a cosine
    correlation threshold and/or a distance threshold and the resulting
    graph is visualized using a force-directed graph layout algorithm.
    VeloViz can help ensure that relationships between cell states are
    reflected in the 2D embedding, allowing for more reliable
    representation of underlying cellular trajectories.

There are 13 new data experiment packages in this release of Bioconductor.

  • curatedTBData The curatedTBData is an R
    package that provides standardized, curated tuberculosis(TB)
    transcriptomic studies. The initial release of the package contains
    49 studies. The curatedTBData package allows users to access
    tuberculosis trancriptomic efficiently and to make efficient
    comparison for different TB gene signatures across multiple
    datasets.

  • easierData Access to internal data required
    for the functional performance of easier package and exemplary
    bladder cancer dataset with both processed RNA-seq data and
    information on response to ICB therapy generated by Mariathasan et
    al. “TGF-B attenuates tumour response to PD-L1 blockade by
    contributing to exclusion of T cells”, published in Nature, 2018
    doi:10.1038/nature25501. The
    data is made available via
    IMvigor210CoreBiologies
    package under the CC-BY license.

  • GSE103322 Single cell RNA-Seq data for 5902
    cells from 18 patients with oral cavity head and neck squamous cell
    carcinoma available as GEO accession [GSE103322]
    (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322).
    GSE103322 data have been parsed into a SincleCellExperiment object
    available in ExperimentHub.

  • GSE159526 19 term and 9 first trimester
    placental chorionic villi and matched cell-sorted samples ran on
    Illumina HumanMethylationEPIC DNA methylation microarrays. This
    data was made available on GEO accession
    GSE159526.
    Both the raw and processed data has been made available on
    code{ExperimentHub}. Raw unprocessed data formatted as an
    RGChannelSet object for integration and normalization using minfi
    and other existing Bioconductor packages. Processed normalized data
    is also available as a DNA methylation code{matrix}, with a
    corresponding phenotype information as a code{data.frame} object.

  • nullrangesData Provides datasets for
    the nullranges package vignette, in particular example datasets for
    DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF
    genomic interactions. These are used to demonstrate generation of
    null hypothesis feature sets, either through block bootstrapping or
    matching, in the nullranges vignette. For more details, see the
    data object man pages, and the R scripts for object construction
    provided within the package.

  • NxtIRFdata NxtIRFdata is a companion
    package for NxtIRF, which is an IRFinder- based R package for
    Intron Retention and Alternative Splicing quantitation for RNA-seq
    BAM files. NxtIRFdata contains Mappability files required for the
    generation of human and mouse references. NxtIRFdata also contains
    a synthetic genome reference and example BAM files used to test
    NxtIRF. BAM files are based on 6 samples from the Leucegene dataset
    provided by NCBI Gene Expression Omnibus under accession number
    GSE67039.

  • plotgardenerData This is a
    supplemental data package for the plotgardener package. Includes
    example datasets used in plotgardener vignettes and example raw
    data files. For details on how to use these datasets, see the
    plotgardener package vignettes.

  • RLHub | RLHub provides a convenient interface to
    the processed data provided within RLSuite, a tool-chain for
    analyzing R-loop-mapping data sets. The primary purpose of RLHub is
    to serve the processed data sets required by the RLSeq R package
    and the RLBase web service. Additionally, RLHub provides a
    stand-alone R interface to these data, benefiting users who are
    addressing questions related to R-loop regions (RL-Regions),
    R-loop-binding proteins (RLBPs), R-loop co-localizing factors, and
    the differences between R-loop-mapping methods. The full
    data-generating protocol is found here:
    github.com/Bishop-Laboratory/RLBase-data.

  • scanMiRData This package contains
    companion data to the scanMiR package. It contains KdModel (miRNA
    12-mer binding affinity models) collections corresponding to all
    human, mouse and rat mirbase miRNAs. See the scanMiR package for
    details.

  • scATAC.Explorer This package provides
    a tool to search and download a collection of publicly available
    single cell ATAC-seq datasets and their metadata. scATAC-Explorer
    aims to act as a single point of entry for users looking to study
    single cell ATAC-seq data. Users can quickly search available
    datasets using the metadata table and download datasets of interest
    for immediate analysis within R.

  • spatialDmelxsim Spatial allelic
    expression counts from Combs & Fraser (2018), compiled into a
    SummarizedExperiment object. This package contains data of allelic
    expression counts of spatial slices of a fly embryo, a Drosophila
    melanogaster x Drosophila simulans cross. See the CITATION file for
    the data source, and the associated script for how the object was
    constructed from publicly available data.

  • TabulaMurisSenisData This package
    provides access to RNA-seq data generated by the Tabula Muris Senis
    project via the Bioconductor project. The data is made available
    without restrictions by the Chan Zuckerberg Biohub. It is provided
    here without further processing, collected in the form of
    SingleCellExperiment objects.

  • tuberculosis The tuberculosis
    R/Bioconductor package features tuberculosis gene expression data
    for machine learning. All human samples from GEO that did not come
    from cell lines, were not taken postmortem, and did not feature
    recombination have been included. The package has more than 10,000
    samples from both microarray and sequencing studies that have been
    processed from raw data through a hyper-standardized, reproducible
    pipeline.

There are 10 new annotation packages in this release of Bioconductor.

  • chromhmmData Annotation files of the formatted
    genomic annotation for ChromHMM. Three types of text files are included the
    chromosome sizes, region coordinates and anchors specifying the transcription
    start and end sites. The package includes data for two versions of the genome
    of humans and mice.

  • CTCF Genomic coordinates of predicted CTCF binding sites
    with motif MA0139.1 (Jaspar), in BED format. With strand orientation
    (directionality of binding). Human (hg19, hg38) and mouse (mm9, mm10)
    genomes. The binding sites were detected using the FIMO tool of the MEME suite
    using default settings. Extra columns include motif name (MA0139.1), score,
    p-value, q-value, and the motif sequence.

  • excluderanges Genomic coordinates of problematic
    genomic regions that should be avoided when working with genomic data. GRanges
    of exclusion regions (formerly known as blacklisted), centromeres, telomeres,
    known heterochromatin regions, etc. (UCSC ‘gap’ table data). Primarily for
    human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.

  • GeneSummary This package provides long description of
    genes collected from the RefSeq database. The text in “COMMENT” section
    started with “Summary” is extracted as the description of the gene. The long
    text descriptions can be used for analysis such as text mining.

  • ontoProcData This package manages rda files of
    multiple ontologies that are used in the ontoProc package. These ontologies
    were originally downloaded as owl or obo files and converted into Rda
    files. The files were downloaded at various times but most of them were
    downloaded on June 22 2021.

  • rGenomeTracksData rGenomeTracksData is a
    collection of data from pyGenomeTracks project. The purpose of this data is
    testing and demonstration of rGenomeTracks. This package include 14 sample
    file from different genomic and epigenomic file format.

  • scAnnotatR.models Pretrained models for
    scAnnotatR package. These models can be used to automatically classify several
    (immune) cell types in human scRNA-seq data.

  • synaptome.data The package provides access to the
    copy of the Synaptic proteome database. It was designed as an accompaniment
    for Synaptome.DB package. Database provides information for specific genes and
    allows building the protein-protein interaction graph for gene sets, synaptic
    compartments, and brain regions.

  • synaptome.db The package contains local copy of the
    Synaptic proteome database. On top of this it provide a set of utility R
    functions to query and analyse its content. It allows extraction of
    information for specific genes and building the protein-protein interaction
    graph for gene sets, synaptic compartments, and brain regions.

  • TxDb.Athaliana.BioMart.plantsmart51
    Exposes an annotation databases generated from BioMart by exposing these as
    TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The
    BioMart plantsmart release number is 51.

There is 1 new workflow package in this release of Bioconductor.

  • GeoMxWorkflows Workflows for use with
    NanoString Technologies GeoMx Technology. Package provides
    bioconductor focused workflows for leveraging existing packages
    (e.g. GeomxTools) to process, QC, and analyze the data.

There are no new online books.

                   Changes in version 1.41.1                        
  • vignette: select subset ALL data without replacement
             Changes in version 1.65.3 (2021-09-22)                 

SOFTWARE QUALITY

SOFTWARE QUALITY

BUG FIXES

  • The package did not install on macOS with the M1 chip with error:
    “use of
    undeclared identifier ‘finite’; did you mean ‘isfinite’?”. This issue
    goes
    back to 2014, when macOS produced “warning: ‘finite’ is deprecated:
    first
    deprecated in OS X 10.9 [-Wdeprecated-declarations]. isOk =
    finite(x);”.
    Patched by using isfinite() instead of finite().
             Changes in version 3.3.4 (2021-09-16)                  
  • Fix issue with PCA plots not working as expected
  • Ensure NMRExperiment names are not duplicated in a dataset (closes
    #44)
  • Fix issue with some title file formatting in Bruker samples (closes
    #46)
  • Export groups in to_ChemoSpec
  • License since AlpsNMR was released has alwayd been MIT as stated in
    the bioinformatics paper
             Changes in version 1.3.2 (2021-08-05)                  
  • Add rmarkdown to the suggests field

               Changes in version 1.3.1 (2021-08-05)                  
    
  • Add warnings for small sample size.

                    Changes in version 3.1.0                        

MAJOR UPDATES

  • (3.1.2) In accordance with the deprecated caching location, upgraded
    to
    error/defunct from warning/deprecated in preparaion for removal of
    dependency next release

USER-VISIBLE MODIFICATIONS

  • (3.1.1) If there is a duplicate entry in the hub cache for a
    resource, hub
    code will no longer produce an ERROR. If the duplicate resource was
    not
    requested the duplicate is ignored. If the duplicate resource is
    requested,
    produce a warning for corrupt cache and continue with first found
    entry.

  • (3.1.3) Fix typo in message display

  • (3.1.5) Deprecate the display,Hub-method

BUG CORRECTION

  • (3.1.7) Fix ERROR message for out-dated orgDbs
                    Changes in version 1.6.0                        

NEW FEATURES

  • (v. 1.5.5) add repository() to return the binary repository
    location, if available.

  • (v. 1.5.7) drs_stat() and drs_cp() support signed URLs

USER VISIBLE CHANGES

  • (v. 1.5.2) drs_stat() uses multiple cores (on non-Windows) to
    enhance performance

  • (v. 1.5.6) install() delegates to BiocManager::install(), providing
    more flexibility (e.g., installing from GitHub) and robustness.

  • (v. 1.5.7) drs_stat() returns fields more selectively.

                    Changes in version 1.4.0                        

New Features

  • (v. 1.3.2) Support _bookdown.yml – name and order vignettes
             Changes in version 1.7.3 (2021-08-01)                  
  • Fixed the typo in vignettes.

               Changes in version 1.7.2 (2021-07-31)                  
    
  • Fixed the issues of using 3’most bam file (generate using
    ThreeMostPairBam) in PASEXP_IPA.

               Changes in version 1.7.1 (2021-07-09)                  
    
  • Fixed the missing SS column issues in PAS2GEF.

             Changes in version 3.23.1 (2021-08-19)                 

DOCUMENTATION

  • Update several citation URLs that were either broken or redirects
    elsewhere.
             Changes in version 1.10.2 (2021-07-13)                 
  • Bug fix affecting {artmsAnalysisQuantifications()}

  • Allow {artmsAnalysisQuantifications()} to process previous versions
    of artMS

  • Change Extension of {artms_sessionInfo_quantification} file from
    {.txt} to {.log}

  • New parameters available in {artmsQuantification()}, including:
    • Parameter {printTables}. Default {TRUE}, prints tables. FALSE
      otherwise.
    • Parameter {return_results_object}. If TRUE, it returns a list of
      data frames with MSstats results. Default is FALSE
    • If both {printTables} and {printPDF} are FALSE, then
      {return_results_object} becames TRUE and a list of data frames is
      returned
  • Change default parameters of the configuration files: less verbose

               Changes in version 1.10.1 (2021-06-30)                 
    
  • Addressing major changes in MSstats
    • R version larger than 4.1 is now required
    • Fractions: the option “Fractions” is removed from the configuration
      file. If fractions are present, the user must include a “Fraction”
      column in the keys.txt file, which artMS will detect automatically.
    • {artmsQualityControlEvidenceBasic}: fraction parameter no longer
      required (automatically detected from the keys file)
    • {keys.txt}: use {Fraction} instead of {FractionKey}
  • External packages used exclusively by the
    {artmsAnalysisQuantifications} function are not required. Those
    packages will have to be installed before running this function.

  • {artmsAvgIntensityRT}: argument {species} is not longer required

  • Example datasets:
    • {artms_data_ph_evidence}: the size has been significantly reduced
      (bioconductor requirement). Only two biological replicates and 1/20
      of the lines selected randomly. Including only 36 columns from the
      original evidence file
    • {artms_data_ph_msstats_results}: output from running
      {artmsQuantification} on the full version of the evidence file,
      including 4 biological replicates (instead of the reduced version
      available in the package)
    • {artms_data_ph_msstats_modelqc}: output from running
      {artmsQuantification} on the full version of the evidence file,
      including 4 biological replicates (instead of the reduced version
      available in the package)
                    Changes in version 2.3.1                        

BUG FIXES

  • Function vecMin inside .filterJunctionBySample threw an error if
    every element in counts vector was larger than the filter. Now works
    correctly using pmin instead.
                   Changes in version 1.17.1                        
  • Fix the issue that NA is generated when no data available for
    TSSEscore.
            Changes in version 0.99.36 (2021-08-01)                 

USER VISIBLE CHANGES

  • Submission of the first version to the Bioconductor project.
             Changes in version 2.5.7 (2021-10-05)                  
  • Fix tests for BiocParallel behaviour.

               Changes in version 2.5.6 (2021-10-05)                  
    
  • Revert 2.5.5 changes; add expectation to empty tests.

               Changes in version 2.5.5 (2021-08-24)                  
    
  • Bugfix tests with change in BiocParallel behaviour

               Changes in version 2.5.4 (2021-08-24)                  
    
  • Ensure ordering of genes in chains is consistent with input data
    when using divide and conquer

               Changes in version 2.5.3 (2021-08-11)                  
    
  • Add GeneExponent and CellExponent settings for divide and conquer.

               Changes in version 2.5.2 (2021-08-11)                  
    
  • Add better spacing around EFDR message.

  • Fix ggplot2 guide=FALSE warnings

  • Remove an errant browser() call

               Changes in version 2.5.1 (2021-05-19)                  
    
  • Add error condition for unnamed cells.

                    Changes in version 1.3.1                        

Minor improvements and fixes

Minor improvements and fixes

  • Added information to documentation.
  • getRDS() updated with new URL.
             Changes in version 0.99.4 (2021-10-15)                 
  • Changed stats::coef to stats4::coef

               Changes in version 0.99.3 (2021-10-15)                 
    
  • Added the plotIt = FALSE option for plotRMSE function

  • Added some more explanations into the “Goodness of Fit” chapter

  • fitNB, fitZINB, fitHURDLE, fitZIG, and fitDM functions now work with
    both phyloseq object or count matrices

               Changes in version 0.99.2 (2021-10-11)                 
    
  • Changed dependency from R 4.0.0 to 4.1.0

  • Added example for iterative_ordering() function

  • Removed the usage of @ to access object’s slot in the vignette

  • Removed a suppressMessages() and a suppressWarnings() from
    createTIEC()

  • Added verbosity to createTIEC() function

  • Added NEWS file

               Changes in version 0.99.1 (2021-10-04)                 
    
  • Removed unnecessary files

               Changes in version 0.99.0 (2021-09-29)                 
    
  • Bumped version for submission to Bioconductor

  • Added README.md file

                   Changes in version 2.18.1                        
  • Possibility to retrieve single cell full length RNA-Seq from
    Bgee 15.0 and after

  • Possibility to filter data based on sex and strain for Bgee
    15.0 and after

  • Possibility to filter on cellTypeId for single cell full length
    RNA-Seq for Bgee 15.0 and after

  • Added pValue in the download files

                   Changes in version 0.99.10                       
  • coverageOverRanges() now supports mean and sum as combination method.
    Dpending
    on the returnOption, mean/ sum are computed over ranges or
    replicates.

                     Changes in version 0.99.9                        
    
  • BSFDataSet() and BSFDataSetFromBigWig() now check the path to the
    bigwig
    files in the meta data for potential duplicates

  • coverageOverRanges() now supports also ranges with different width,
    if
    returnOption = merge_positions_keep_replicates

  • Fix bug in makeBindingSites(); The minWidth parameter is now
    implemented as
    true lower boundary (>= instead of >). The default has changed from 2
    to 3.

  • Fix description in makeBindingSites(); The minCrosslinks parameter
    describes
    the number of positions covered by crosslink events, instead of the
    total
    number of crosslinks.

  • Updated color scheme in rangeCoveragePlot(); and changed position of
    indicator
    box

  • Updated visual of reproducibiliyCutoffPlot() function

                     Changes in version 0.99.8                        
    
  • Updated coverageOverRange(), Function now does support different
    output
    formats, summarizing the coverage differently over range, replicates
    and
    condition

                     Changes in version 0.99.1                        
    
  • Fix bugs for Bioconductor submission

               Changes in version 0.99.0 (2021-05-15)                 
    
  • Submitted to Bioconductor

                    Changes in version 1.29                         

NEW FEATURES

  • (1.29.10) Check for Sys.setenv and
    suppressWarnings/suppressMessages

  • (1.29.8) Check for sessionInfo / session_info in vignette code.

  • (1.29.5) Check for installation calls in vignette code.

  • (1.29.1) Check for install() function calls in R code.

BUG FIXES

  • (1.29.14) Various internal improvements to the codebase.

  • (1.29.12) Checks on class membership code now include is() ==
    grammar.

  • (1.29.6) Use appropriate input (pkgdir) to internal checking
    functions.

  • (1.29.3) Add unit tests for legacy function searches.

  • (1.29.2) rename internal function from checkIsPackageAlreadyInRepo to
    checkIsPackageNameAlreadyInUse

                     Changes in version 2.1                         

MAJOR UPDATES

  • (2.1.1) Change caching location warning/deprecation to an ERROR in
    preparation for removal of dependency next release.
                    Changes in version 1.28                         

USER VISIBLE CHANGES

  • (v 1.27.3) Setting progressbar = TRUE for SnowParam() or
    MulticoreParam() changes the default value of tasks from 0 to
    .Machine$integer.max, so that progress on each element of X is
    reported.

  • (v 1.27.3) tasks greater than length(X) are set to
    length(X). Thus .Machine$integer.max, for instance, assures
    that each element of X is a separate task.

  • (v 1.27.5) Use of random numbers is robust to the distribution
    of jobs across tasks for SerialParam(), SnowParam(), and
    MulticoreParam(), for both bplapply() and bpiterate(), using the
    RNGseed= argument to each *Param(). The change is NOT backward
    compatible – users wishing to exactly reproduce earlier results
    should use a previous version of the package.

  • (v 1.27.8) Standardize SerialParam() construct to enable setting
    additional fields. Standardize coercion of other BiocParallelParam
    types
    (e.g., SnowParam(), MulticoreParam()) to SerialParam() with
    as(., “SerialParam”).

  • (v. 1.27.9) By defualt, do not only run garbage collection
    after every call to FUN(), except under MulticoreParam(). R’s
    garbage collection algorithm only fails to do well when forked
    processes (i.e., MulticoreParam) assume that they are the only
    consumers of process memory.

  • (v 1.27.11) Developer-oriented functions bploop.*() arguments
    changed.

  • (v 1.27.12) Ignore set.seed() and never increment the global random
    number stream. This reverts a side-effect of behavior introduced in
    v.
    1.27.5 to behavior more consistent with version 1.26.

  • (v 1.27.16) Better BPREDO support for previously started BPPARAM, and
    ‘transient’ BPPARAM without RNGseed.

BUG FIXES

                   Changes in version 1.12.0                        

NEW FEATURES

  • biocRevDepEmail sends an email to several downstream maintainers to
    notify them of a deprecated package.

  • biocBuildEmail allows deprecation notices using the template in the
    inst folder. Use templatePath() to see available templates by
    their
    location.

  • PackageStatus indicates whether a package is slated for
    ‘Deprecation’ by checking the meat-index.dcf file.

  • pkgDownloadStats provides the download statistics table for a
    particular package.

BUG FIXES

  • biocDownloadStats includes all types of Bioconductor packages

  • biocBuildReport improved to work on old-rel, release, and devel
    Bioconductor versions

                   Changes in version 2.22.0                        

USER-VISIBLE CHANGES

  • Added section to HTML vignette regarding accessibility considerations
    when creating plots and figures.

BUG FIXES AND IMPROVEMENTS TO HTML STYLE

  • Improved navigation for screen readers by adding role=’link’ and
    tabindex=’0’ to elements in the table of contents. TOC navigation
    can also
    be followed by pressing “Enter” when selected in addition to clicking
    with
    the cursor.

  • Addressed further styling issues for code blocks, introduced by
    changes
    in rmarkdown. This time re-introducing padding around <pre> tags.

                    Changes in version 1.3.8                        

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEW FEATURES

  • use_bioc_github_action() now uses the AnVIL-powered package
    binaries, which greatly speed up the dependency installation steps
    in the docker (Linux) GitHub Actions builds. Details are available
    in Nitesh Turaga’s BioC2021 slides
    github.com/nturaga/bioc2021-bioconductor-binaries.
                   Changes in version 1.61.0                        

ENHANCEMENT

  • (1.61.1) Added Spatial, SpatialData, SpatialWorkflow to distinguish
    from SigleCell
             Changes in version 1.1.16 (2021-10-19)                 
  • Update documentation.

  • Add ORCID for Alexis.

               Changes in version 1.1.15 (2021-10-18)                 
    
  • Correct getUrlContent() to handle binary files.

               Changes in version 1.1.14 (2021-10-17)                 
    
  • Factorize RCurl calls into global functions.

  • Disable warnings in calls to readLines() when using base::url().

  • Catch errors when trying to set locale.

  • Correct some tests.

               Changes in version 1.1.13 (2021-10-12)                 
    
  • Make custom persistent the cache the default, following slowness with
    BiocFileCache in biodbHmdb.

  • Remove useless bib refs in vignettes/references.bib.

  • Add session info in vignettes.

  • Add ORCID, URL and BugReports.

  • Add an install section in main vignette.

               Changes in version 1.1.12 (2021-10-09)                 
    
  • Switch back to custom implementation of persistent cache, following
    errors with BiocFileCache on Windows and also slowness with HMDB.

               Changes in version 1.1.11 (2021-10-07)                 
    
  • Decompose test test.collapseRows() because of error on Bioconductor
    not reproduced on local computer.

               Changes in version 1.1.10 (2021-09-30)                 
    
  • Disable UniProt request test: it fails (result is NA) for reason
    unknown only on Bioconductor Linux server during “R CMD check”. Works
    fine on local computer.

               Changes in version 1.1.9 (2021-09-28)                  
    
  • Correct handling of wrong URL with base::url().

               Changes in version 1.1.8 (2021-09-28)                  
    
  • Correct bug of UniProt request on Windows.

               Changes in version 1.1.7 (2021-09-23)                  
    
  • Ignore build folder when building package.

  • Update documentation.

  • Correct setting of R_ENVIRON_USER when building.

               Changes in version 1.1.6 (2021-09-14)                  
    
  • Update documentation.

               Changes in version 1.1.5 (2021-09-13)                  
    
  • Correct bug in return type of BiodbRequestScheduler::sendRequest().

  • Correct encoding of test reference filenames.

               Changes in version 1.1.4 (2021-09-12)                  
    
  • Allow to set the test reference folder directly into
    runGenericTests(). This
    is now necessary for running generic tests in extension packages.

               Changes in version 1.1.3 (2021-09-12)                  
    
  • Set package name when calling runGenericTests() in order to find test
    ref
    files the correct way, by calling system.file().

               Changes in version 1.1.2 (2021-09-09)                  
    
  • Use BiocFileCache for the persistent cache system.

  • Switch to R6.

  • Define do…() private methods to be redefined in subclasses, instead
    of
    redefining public methods defined inside super class.

  • Use now local entry files for testing parsing of entry fields.

               Changes in version 1.1.1 (2021-06-10)                  
    
  • Allow skipping of some fields when testing searchForEntries().

  • Move test reference entries folder from tests/testthat/res to
    inst/testref.

  • Move long tests folder from tests/long to longtests and enable
    Bioconductor
    long tests.

               Changes in version 1.0.4 (2021-06-09)                  
    
  • Bug fix: correct call to logger in BiodbPersitentCache class.

               Changes in version 1.0.3 (2021-05-26)                  
    
  • Bug fix: correct generic test of searchForEntries(), allowing testing
    with NA
    value.

               Changes in version 1.0.2 (2021-05-23)                  
    
  • Bug fix: correct return type of searchForEntries(), which now returns
    always
    a character vector and never NULL.

               Changes in version 1.0.1 (2021-05-20)                  
    
  • Bug fix: correct some calls to logging functions that raised a
    warning.

             Changes in version 0.99.6 (2021-10-12)                 
  • Rename vignette.

  • Add session info and install section in vignette.

  • Use importFrom.

               Changes in version 0.99.5 (2021-10-07)                 
    
  • Write description on multiple lines.

  • Put comment banners to indicate public and private sections in R6
    class.

               Changes in version 0.99.4 (2021-09-28)                 
    
  • Correct list index in vignette.

               Changes in version 0.99.3 (2021-09-28)                 
    
  • Complete all chapters in README.

  • Remove ‘foo’ names in vignette.

               Changes in version 0.99.2 (2021-09-23)                 
    
  • Define R_BUILD_TAR in makefile to build on UNIX.

               Changes in version 0.99.1 (2021-09-23)                 
    
  • Upgrade maintenance files.

  • Ignore build folder.

               Changes in version 0.99.0 (2021-09-16)                 
    
  • Submitted to Bioconductor

             Changes in version 0.99.4 (2021-10-18)                 
  • When reading the zipped database, take the only XML file available,
    ignoring other files.

               Changes in version 0.99.2 (2021-10-12)                 
    
  • Add ORCID, URL and BugReports.

  • Add session info and install sections in vignette.

  • Corrected indentations in vignette.

               Changes in version 0.99.1 (2021-09-29)                 
    
  • Slight corrections for Bioconductor submission.

               Changes in version 0.99.0 (2021-07-16)                 
    
  • Submitted to Bioconductor

             Changes in version 0.99.4 (2021-10-13)                 
  • Merge both vignettes into a single one.

  • Remove messages from magick package.

               Changes in version 0.99.3 (2021-10-12)                 
    
  • Add install section in vignette.

  • Use importFrom.

  • Add ORCID, URL and BugReports.

               Changes in version 0.99.2 (2021-10-12)                 
    
  • Rename main vignette file.

  • Add reference.

  • Add session info in vignettes.

               Changes in version 0.99.1 (2021-09-28)                 
    
  • Made some corrections for submitting to Bioconductor.

               Changes in version 0.99.0 (2021-09-16)                 
    
  • Submitted to Bioconductor

             Changes in version 0.99.3 (2021-10-18)                 
  • Remove deprecated slow frequency of request send.

               Changes in version 0.99.2 (2021-10-12)                 
    
  • Add ORCID, URL and BugReports.

  • Add citation into vignette.

  • Add install and session info sections to vignette.

               Changes in version 0.99.1 (2021-09-29)                 
    
  • Complete README.

  • Slight corrections for Bioconductor submission.

  • Add generated documentation files.

               Changes in version 0.99.0 (2021-09-16)                 
    
  • Submitted to Bioconductor.

             Changes in version 0.99.4 (2021-10-12)                 
  • Add session info and install section in vignette.

  • Rename vignette.

  • Use importFrom.

  • Add ORCID, URL and BugReports.

               Changes in version 0.99.3 (2021-10-11)                 
    
  • Show progress when filtering results in geneSymbolToUniprotIds().

               Changes in version 0.99.2 (2021-10-03)                 
    
  • Use biodb 1.1.10.

               Changes in version 0.99.1 (2021-09-23)                 
    
  • Ignore build folder when building package.

  • Add documentation.

               Changes in version 0.99.0 (2021-09-16)                 
    
  • Submitted to Bioconductor

                   Changes in version 2.50.0                        

MINOR CHANGES

  • useMart() and listMarts() will warn users if using http to access
    Ensembl. https will be enforced by Ensembl from late 2021.

BUG FIXES

  • Address issue where checking the list of Ensembl Archives would stop
    all queries from working if the main www.ensembl.org site was
    unavailable.

  • Fix bug introduced in getSequence() where asking for flanking
    sequences
    resulted in an invalid query.

  • The argument ‘host’ is no longer ignored in useEnsembl() (Thanks to
    forum
    user “A” – support.bioconductor.org/p/9139019/)

                    Changes in version 1.0.0                        
  • Initial release of the BioPlex package
                   Changes in version 1.17.0                        
  • Removal of future and doFuture for simplification of
    parallelization. All
    control of parallel computation now done through BiocParallel.
                   Changes in version 0.99.0                        

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.

SIGNIFICANT USER-VISIBLE CHANGES

            Changes in version 0.99.18 (2020-06-01)                 
  • Importing “assay<-“ in the NAMESPACE

              Changes in version 0.99.17 (2020-06-01)                 
    
  • Correcting the import of dependencies

              Changes in version 0.99.16 (2020-06-01)                 
    
  • Avoiding the overlapping when loading dependencies

              Changes in version 0.99.15 (2020-06-01)                 
    
  • Removing the redundant print and summary function

              Changes in version 0.99.14 (2020-06-01)                 
    
  • Modifying the output of BUSseq_MCMC as a SingleCellExperiment object
    and allowing the input as that object as well

              Changes in version 0.99.13 (2020-05-15)                 
    
  • Modifying the running example

              Changes in version 0.99.12 (2020-05-15)                 
    
  • Revising the random number generator for MacOS

              Changes in version 0.99.11 (2020-05-15)                 
    
  • Debugging for MacOS

              Changes in version 0.99.10 (2020-05-15)                 
    
  • Continuing to debug for MacOS

               Changes in version 0.99.9 (2020-05-15)                 
    
  • Modifying the warnings when building on MacOS

               Changes in version 0.99.8 (2020-05-15)                 
    
  • Correcting the usage of OS macro

               Changes in version 0.99.7 (2020-05-14)                 
    
  • Updating th source code for MacOS

               Changes in version 0.99.6 (2020-05-13)                 
    
  • Downsizing the example dataset to avoid reaching the time limit of
    check

               Changes in version 0.99.5 (2020-05-12)                 
    
  • Adding the macro for Mac in the source code

  • Shortening the vignettes

  • Adding Watched Tags BUSseq to my profile

               Changes in version 0.99.4 (2020-05-12)                 
    
  • Correct R version dependency

  • Solve the warnings by missing parenthesees

               Changes in version 0.99.3 (2020-05-08)                 
    
  • Set LazyData as TRUE for building vignette

               Changes in version 0.99.2 (2020-05-08)                 
    
  • Correctly pushing by Git

               Changes in version 0.99.1 (2020-05-07)                 
    
  • Revised the warnings by R CMD check, including adding parentheses in
    src and R dependency in DESCRIPTION

               Changes in version 0.99.0 (2020-05-04)                 
    
  • Submitted to Bioconductor

                   Changes in version 0.99.0                        

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.
                    Changes in version 2.0.0                        

BACKWARDS-INCOMPATIBLE CHANGES

  • The CAGEset class is removed.

  • Accessors using plain data.frame formats are removed.

  • Modifier functions return the object instead of silently modifying it
    in the global environment. Thus, you can use R pipes (|>).

  • Removed export function that unconditionally wrote files to the
    working directory, such as exportCTSStoBedGraph. As a replacement
    a
    new converter is provided, exportToBrowserTrack, that produces
    UCSCData objects that the user can then wite to files using the
    rtracklayer package.

  • Removed the extractExpressionClass function, as the information is
    easily accessible from within the CTSS or ConsensusClusters
    objects.

NEW FEATURES

  • CTSSnormalizedTpmGR and CTSStagCountGR now accept "all" as a
    special
    sample name to return them all in a GRangesList object.

  • Plot interquantile width and expression clusters with ggplot2.

BUG FIXES

  • Corrected the getExpressionProfiles function to accept CAGEexp
    objects.

  • Updated the exampleCAGEexp object to contain expression classes.

  • Restore paraclu support for CAGEexp objects.

  • Corrected a bug in aggregateTagClusters that was causing
    mislabelling
    of tag clusters (PR#42).

  • Prevent plotReverseCumulatives from crashing when values are not in
    range. (PR#43).

                   Changes in version 2.11.3                        

BUG FIXES

BUG FIXES

BUG FIXES

  • Use as(x, ‘DFrame’) instead of as(x, ‘DataFrame’)

  • Fix logical length > 1 error in ‘segmentationTest()’

             Changes in version 1.16.0 (2021-10-14)                 

New Features

                    Changes in version 2.6.0                        

New features

  • A study’s build status can be obtained from getStudies(), which has
    replaced data(‘studiesTable’).
  • Partial loading of data files supported. A warning is emitted when
    a
    data file is not able to be loaded in cBioDataPack.
  • cBioPortalData checks the data(studiesTable) to verify that study
    datasets are building, otherwise provide a message in interactive
    sessions.
             Changes in version 1.9.3 (2021-10-04)                  
                    Changes in version 0.0.1                        
  • Added a NEWS.md file to track changes to the package.
                    Changes in version 1.5.4                        
                   Changes in version 0.99.1                        
                   Changes in version 3.27.7                        
  • Fix the error “!anyNA(m32) is not TRUE” in seqlevelsStyle is not
    handled.

                     Changes in version 3.27.6                        
    
  • Fix the error “pvalue” undefined columns selected in enrichmentPlot

                     Changes in version 3.27.5                        
    
  • update documentation of pipeline.rmd

                     Changes in version 3.27.4                        
    
  • use formatSeqnames function to handle the error from seqlevelsStyle:
    “cannot switch some of GRCm38’s seqlevels from NCBI to UCSC style”

                     Changes in version 3.27.3                        
    
  • use formatSeqnames function to handle the error from seqlevelsStyle:
    “!anyNA(m31) is not TRUE “

                     Changes in version 3.27.2                        
    
  • add keepExonsInGenesOnly for genomicElementDistribution

  • add upstream and downstream for assignChromosomeRegion function when
    define promoter and downstream regions.

                     Changes in version 3.27.1                        
    
  • Add the possibility of find overlaps by percentage covered of
    interval
    for function findOverlapsOfPeaks

                   Changes in version 1.29.2                        
  • extend functions for plotting peak profiles to support other types
    of bioregions (2021-10-15, Fri, @MingLi-292, #156, #160, #162, #163)

                     Changes in version 1.29.1                        
    
  • add example for seq2gene function (2021-05-21, Fri)

                    Changes in version 1.1.3                        

Overview:

New functionalities:

Overview:

New functionalities:

                   Changes in version 2.14.0                        
  • Upsampling and downsampling to equalise class sizes added.
             Changes in version 0.99.0 (2021-01-22)                 
  • Submitted to Bioconductor
                    Changes in version 1.7.0                        
  • Bug fixes: Change in example of computeCliques function.
                   Changes in version 1.32.0                        

DEPRECATION NOTICE

  • Note that clonotypeR is depreacted. Please adopting it or using a
    different package.
                    Changes in version 4.1.4                        
  • import yulab.utils (2021-08-20, Fri)

                      Changes in version 4.1.3                        
    
  • Remove Human Gut Microbiome dataset as the functionalities are
    provided in github.com/YuLab-SMU/MicrobiomeProfiler
    (2021-08-15, Sun)

                      Changes in version 4.1.2                        
    
  • update citation and DESCRIPTION (2021-08-15, Sun)
  • update kegg_species.rda and allow online download using KEGG api
    (2021-08-14, Sat)

                      Changes in version 4.1.1                        
    
  • add citation (new paper published on The Innovation) (2021-07-04,
    Sun)
             Changes in version 1.5.2 (2021-10-04)                  
  • clustify_lists() support for output of overlapping genes
    (details_out = TRUE)

  • Added truncated mean and trimean modes to average_clusters()

               Changes in version 1.5.1 (2021-08-04)                  
    
  • clustify_lists() support for uneven number of markers

  • Deprecated SeuratV2 support

                    Changes in version 1.7.4                        

MINOR

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

  • Fixed: parsing some VCFs produced an unexpected error

MINOR

MINOR

                    Changes in version 1.9.1                        
  • add uniquely_high_in_one_group method in get_signatures().

  • add compare_partitions().

  • parallel computing is implemented with foreach + doParallel

                      Changes in version 1.9.0                        
    
  • use row/column* family functions in adjust_matrix() to reduce the
    memory
    usage as well as improve the speed.

                    Changes in version 2.9.4                        
  • fixed a bug of missing right annotation legends for vertically
    concatenated heatmaps.

  • Legend(): support border to be set to asis.

  • Rasterization: the default maximal size for temporary image is set to
    30000 px (both for width and height).

  • add a new argument beside in anno_barplot() to position bars
    beside each other.

  • add plot() method for Heatmap and HeatmapList classes.

  • add anno_customize().

                      Changes in version 2.9.3                        
    
  • pheatmap()/heatmap()/heatmap.2(): set default of run_draw to
    FALSE.

  • throw error when the heatmaps (list) are already initialized by
    draw() when adding them.

  • set wrap = TRUE in grid.grabExpr() when capturing the legend
    objects.

  • make_comb_mat(): support GRangesList object as input.

  • legends: fixed a bug of the grid heights were not correctedly
    calculated.

  • discrete annotations: neighbour grids are merged into one single grid
    if they have the
    same values.

  • anno_barplot(): allows to add numbers on top of bars.

  • UpSet(): axis labels are automatically formated for genomic
    coordinates.

  • AnnotationFunction(): add a new argument cell_fun.

  • When the dendrogram height is zero, the corresponding viewport has
    scale (0, 1).

                      Changes in version 2.9.2                        
    
  • fixed a bug of bg_col for transposed matrix in UpSet().

  • print warnings if names of annotations have different orders from the
    matrix row/column names.

                      Changes in version 2.9.1                        
    
  • fixed a bug of editing gTree object where the list element “just” has
    been
    changed to “justification” in recent R versions.

            Changes in version 1.1.002 (2021-08-31)                 

Made the following significant changes

  • Added an internal function .retrieveClustersNumberK to suggest the clusters number to use in lusterCellsInternal().

  • Added suggestedClustersNumber slot in scRNAseq class to retrieve
    this suggested clusters number.

  • Added accessors getSuggestedClustersNumber and
    setSuggestedClustersNumber.

  • Updated all the objects used in examples and tests to have this
    slot.

                    Changes in version 1.5.7                        
  • Add TreatmentResponseExperiment class, a simple wrapper around
    LongTable to make the class syntax more domain specific
  • Add CoreSet2 structure to support creation of CoreSets with the
    modified class structure introducted in BioC 3.13
  • CoreSets can now be made with treatment combination experiments via
    the TreatmentResponseExperiment class!

                      Changes in version 1.5.6                        
    
  • Fix bug in LongTable -> data.table coerce method that was causing
    rows of some assays to be dropped (closes issue #)

                      Changes in version 1.5.5                        
    
  • Fix bug in .distancePointLine where function fails with no
    intercept
    specified (Issue #120)
  • Added support for aggregating an assay inside of a LongTable class
    object
  • Some in-progress updates to the CoreSet constructor which will be
    completed for the Fall release
  • Fixed an error in treatmentNames example
  • Fixed roxygen2 documentation warnings about S4 method documentation
  • Overhauled LongTable coerce methods to use the LongTableDataMapper
    class instead of the deprecated ‘LongTable.config’ attribute

                      Changes in version 1.5.4                        
    
  • Fix bug in $<- and [[<- methods where value was returned instead of
    updated object
  • Fix bug in .sanitize input caused by length > 1 coercing to logical
    vector

                      Changes in version 1.5.3                        
    
  • Fix bug in connectivityScore caused by length > 1 coercing to
    logical vector; this should fix errors in RadioGx and PharmacoGx
    vignettes that were caused by failed R CMD build

                      Changes in version 1.5.2                        
    
  • Add subsetBySample method for CoreSet object; this is the first
    step
    in modularizing the subset methods for reuse in dependent packages
  • Added a CoreSet-utils documentation section to document subset,
    intersect, combine and other set operations for a CoreSet object.

                      Changes in version 1.5.1                        
    
  • Fixed some spelling errors and incorrect code chunk configurations
    in the LongTable vignette
  • Fix bug in .rebuildProfiles where the function fails if
    replicate_id
    is assigned as a rowID column in the LongTable in @sensitivity

                      Changes in version 1.5.0                        
    
  • Bioconductor spring 2021 release
  • Added the DataMapper abstract class
  • Added the LongTableDataMapper concrete class
  • Added the metaConstruct method, for making an S4 object from a
    sub-class of DataMapper
  • Updated LongTable vignette with documentation for the DataMapper
    and
    LongTableDataMapper
  • Refactored various methods to work with a LongTable in
    @sensititivty
  • Refactored various methods to work with a MultiAssayExperiment in
    @molecularProfiles
                   Changes in version 0.99.6                        
  • Bugfix: Open MP was not working correctly because of missing
    compiler flags. For this reason, the Makevars file has been created.
  • Calculation of column ranks now uses matrixStats::colRanks instead
    of an apply statement with base::rank.

                     Changes in version 0.99.0                        
    
  • Added a NEWS.md file to track changes to the package. This is the
    first public version of the package.
                   Changes in version 1.12.0                        

Web server support (optimised to run in ShinyProxy)

  • cTRAP(): new global interface with all cTRAP functionality in one
    place
  • Sessions can be created and loaded via a token or a RDS file
  • Session data is automatically saved in a RDS file to a folder in
    the working directory named based on the current session token
  • Long-running tasks can be performed in the background using the
    Celery task manager via Flower’s REST API and their output is
    automatically loaded in the corresponding session
  • Loading icon in navigation menu when Shiny is busy
  • Use the faster and efficient file format from R package qs instead
    of RDS:
  • Faster download and loading of pre-processed remote files
    (compound molecular descriptors and gene expression and drug
    sensitivity associations)

Bug fixes and minor improvements

  • convertGeneIdentifiers() replaces convertENSEMBLtoGeneSymbols():
  • Use AnnotationHub to convert to gene symbols (instead of biomaRt
    that has been unstable)
  • loadENCODEsamples():
  • New argument to select folder where to download data
  • analyseDrugSetEnrichment():
  • Cross-match more compounds between datasets by discarding
    non-alphanumeric characters and ignoring case
  • Fix incorrect columns used for each dataset when merging
    datasets
  • Visual interface:
  • Fix crash when plotting dataset comparison using values with too
    many zeroes for density estimation
  • Add progress bars for slower tasks
  • Fix crash when using shiny 1.7.0 (avoid malformed, custom UI
    elements)
  • Drug set enrichment analysis interface:
  • Show all drug sets available to (down)load
  • Show loading indicator when loading different drug sets
  • Hide “leading edge” column of the results by default
                   Changes in version 0.99.0                        
  • Submitted marr 0.99.0 to Bioconductor on October 2, 2020.
  • Added a NEWS.md file to track changes to the package.
             Changes in version 1.5.4 (2021-09-17)                  
  • It is not required anymore to specify exactly the right colours

               Changes in version 1.5.3 (2021-09-16)                  
    
  • Added option to read in .h5 files

               Changes in version 1.5.2 (2021-09-15)                  
    
  • Added description on how to handle images with couplet/patchwork

               Changes in version 1.5.1 (2021-05-19)                  
    
  • Bugfix: erroneous dimension setting when legend=NULL

                    Changes in version 3.11                         

API Changes

  • Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
  • All parsers (flowjo/cytobank/diva_to_gatingset) now return
    GatingSet
    based on cytoset rather than ncdfFlowSet
  • Add trans argument to cytobank_to_gatingset to allow overriding of
    transformations from gatingML file (#76)
  • gatingset_to_flowjo now uses a docker image with a compiled
    converter: hub.docker.com/r/wjiang2/gs-to-flowjo
  • Some updates to how flowjo_to_gatingset searches for FCS files
    (#77)
  • Add include_empty_tree option to flowjo_to_gatingset to include
    samples without gates
  • Allow gatingset_to_flowjo to take a path to a GatingSet archive
    directory
  • Add gating_graphGML to replace gating.graphGML method for
    openCyto::gating generic
  • Filter samples by panel when parsing cytobank experiment and add
    ce_get_samples, ce_get_panels

Fixes/internal changes

API Changes

  • Change handling of quad gates according to RGLab/cytolib#16

  • Renaming of methods:

  • openWorkspace -> open_diva_xml, open_flowjo_xml
  • cytobankExperiment -> open_cytobank_experiment
  • cytobank2GatingSet -> cytobank_to_gatingset
  • parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
  • getSampleGroups -> fj_ws_get_sample_groups,
    diva_get_sample_groups
  • getSamples -> fj_ws_get_samples, diva_get_samples
  • getKeywords -> fj_ws_get_keywords
  • getCompensationMatrices -> ce_get_compensations
  • getTransformation -> ce_get_transformations
  • compare.counts -> gs_compare_cytobank_counts

  • Renaming of classes:

  • divaWorkspace -> diva_workspace
  • flowJoWorkspace -> flowjo_workspace

  • Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML
    namespace

Fixes/internal changes

  • Make gatingset_to_cytobank export cytobank ML with attribute
    namespaces
  • Allow diva_to_gatingset to use compensation matrix from xml
  • Pass … args from cytobank_to_gatingset appropriately down to FCS
    parser
  • Fix some issues with scaling of gates parsed from Diva workspace
    (#64)
  • Guard against unsupported transformations being added to GatingSet
    during Diva parsing
  • Switch diva_to_gatingset to using flowjo_log_trans instead of
    logtGml2_trans
  • Fix ported flowUtils::xmlTag to enable self-closing tags
  • Make gating.graphGML lookup tailored gates by FCS name as well as
    file id
  • Add some flexibility to getSpilloverMat used in gatingset_to_flowjo
                    Changes in version 2.6.0                        
  • Major: We fixed a bug in DaMiR.ModelSelect. Now optimal models
    are correctly selected;

  • Major: Now users can plot specific graphs in DaMiR.Allplot and
    we added new plots;

  • Minor: We modified the color scale in corrplot

                    Changes in version 1.3.2                        

NEW FEATURES

  • Fix bugs within plot_sashimi() and enable the visualization of raw
    junction counts.
             Changes in version 1.5.1 (2021-09-01)                  
  • switching from CompQuadForm::davies() to the “saddlepoint” method
    from survey::pchisqsum() for computing quadratic form asymptotic
    p-values
                    Changes in version 2.0.0                        

Changes

  • Some method’s names have been changed to make them easier to
    identify:

  • pscira now is called Weighted Sum (wsum).
  • mean now is called Weighted Mean (wmean).
  • scira now is called Univariate Linear Model (ulm).

  • The column name for tf in the output tibbles has been changed to
    source.

  • Updated documentation for all methods.

  • Updated vignette and README.

  • decouple function now accepts order mismatch between the list of
    methods and the list of methods’s arguments.

  • Moved benchmark branch to a separate repository as its own package:
    github.com/saezlab/decoupleRBench

New features

  • New methods added:

  • Fast Gene Set Enrichment Analysis (fgsea).
  • AUCell.
  • Univariate Decision Tree (udt).
  • Multivariate Decision Tree (mdt).
  • Multivariate Linear Model (mlm).

  • New decoupleR manuscript repository:
    github.com/saezlab/decoupleR_manuscript

  • New consensus score based on RobustRankAggreg::aggregateRanks()
    added when running decouple with multiple methods.

  • New statistic corr_wmean inside wmean.

  • Methods based on permutations or statistical tests now return also
    a
    p-value for the obtained score (fgsea, mlm, ora, ulm, viper, wmean
    and wsum).

  • New error added when network edges are duplicated.

  • New error added when the input matrix contains NAs or Infs.

                      Changes in version 1.1.0                        
    

New features

All new features allow for tidy selection. Making it easier to
evaluate
different types of data for the same method. For instance, you can
specify the columns to use as strings, integer position, symbol or
expression.

Methods

  • New decouple() integrates the various member functions of the
    decoupleR statistics for centralized evaluation.

  • New family decoupleR statists for shared documentation is made up
    of:

  • New run_gsva() incorporate a convinient wrapper for
    GSVA::gsva().
  • New run_mean() calculates both the unnormalized regulatory
    activity and the normalized (i.e. z-score) one based on an
    empirical distribution.
  • New run_ora() fisher exact test to calculate the regulatory
    activity.
  • New run_pscira() uses a logic equivalent to run_mean() with the
    difference that it does not accept a column of likelihood.
  • New run_scira() calculates the regulatory activity through the
    coefficient $beta_1$ of an adjusted linear model.
  • New run_viper() incorporate a convinient wrapper for
    viper::viper().

Converters

  • New functions family convert_to_ variants that allows the
    conversion
    of data to a standard format.
  • New convert_to_() return the entry without modification.
  • New convert_to_gsva() return a list of regulons suitable for
    GSVA::gsva().
  • New convert_to_mean() return a tibble with four columns: tf,
    target, mor and likelihood.
  • New convert_to_ora() returns a named list of regulons; tf with
    associated targets.
  • New convert_to_pscira() returns a tibble with three columns: tf,
    target and mor.
  • New convert_to_scira() returns a tibble with three columns: tf,
    target and mor.
  • New convert_to_viper() return a list of regulons suitable for
    viper::viper()
             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

  • fixed issues with deletions in bf2Vcf()

  • makePrior() adds background on all sites

               Changes in version 1.99.0 (2013-04-30)                 
    

Updates

                    Changes in version 1.3.1                        
  • plot_coverage function has an option “samples” added to allow user to
    visualize a subset of samples.
                   Changes in version 0.20.0                        

BUG FIXES

  • Fix long-standing bugs in dense2sparse():
    • mishandling of NAs/NaNs in input
    • 1D case didn’t work
                    Changes in version 1.0.0                        
             Changes in version 1.9.1 (2021-10-16)                  
  • depecheCoFunction updated to remove traces of the old dAllocate
    functionality
                    Changes in version 1.1.2                        
  • Weights added to the Stouffer’s method
                    Changes in version 2.1.4                        
  • Using non-linear fit to constrain similarity matrix.

  • Recalculate intensity for given peaks.

  • Direct alignment to root is added.

  • Multiple strategies for getting distance matrix and
    tree-agglomeration is added.

  • Remove peaks if not aligned.

                      Changes in version 2.1.0                        
    
  • Added support for IPF based Post-translation Modification alignment.

  • Added Minimum Spanning Tree based alignment for reference-free
    approach.

  • Reintegrate area under the peak for low-confidence peaks.

  • Supporting Savitzky-Golay smoothing while calculating area.

  • Added input to select peptides which to align.

  • Speed improvement in progressive alignment by storing new featues in
    lists instead of data frames.

                    Changes in version 3.3.4                        
  • Fix bFlip issues

  • Fix bug where mode not passed to summarizeOverlaps

  • Add $inter.feature config parameter

                      Changes in version 3.3.2                        
    
  • Re-compute FDR when fold change other than 0 is specified

  • Remove most gc() calls for performance

  • Roll in bugfixes

                   Changes in version 0.99.5                        
  • Data reformatting

                     Changes in version 0.99.4                        
    
  • Revised formatting for Bioconductor submission.
  • Bug fix

                     Changes in version 0.99.3                        
    
  • Reduce size of tutorial data

                    Changes in version 0.99.1                        
    
  • Updated formatting for Bioconductor submission.
  • Reduced size of sample dataset
  • Updated default number of cores to 2

                     Changes in version 0.99.0                        
    
  • Formatted to submit to Bioconductor.
  • Add SingleCellExperiment functionality.
  • Update vignette with SingleCellExperiment example.
                    Changes in version 1.4.1                        
                     Changes in version 1.6                         
  • Vignette Update: Added a ‘Quick-Reference: Seurat<=>dittoSeq’
    section.
  • Build & Test Infrastructure Update: Removed Seurat dependency from
    all build and test materials by removing Seurat code from the
    vignette and making all unit-testing of Seurat interactions
    conditional on both presence of Seurat and successful SCE to Seurat
    cnversion.
  • Bug Fixes:

    1. Fixed dittoFreqPlot calculation machinery to properly
      target all cell types but only necessary groupings for every sample.
      Removed the ‘retain.factor.levels’ input because proper calculations
      treat ‘var’-data as a factor, and groupings data as non-factor.
    2. Allowed dittoHeatmap() to properly ‘drop_levels’ of annotations by
      ensuring ‘annotation_colors’ is not populated with colors for empty
      levels which would be dropped. 3- Made ‘do.label’ machinery of
      scatter plots robust to NAs.
                   Changes in version 3.19.4                        
  • update clusterProfiler citation (2021-09-30, Thu)
  • upate error message of enricher_internal (2021-9-3, Fri)

                     Changes in version 3.19.3                        
    
  • upate DisGeNET and NCG data (2021-8-16, Mon)

                     Changes in version 3.19.2                        
    
  • bug fixed, change ‘is.na(path2name)’ to ‘all(is.na(path2name))’
    (2021-06-21, Mon)

                     Changes in version 3.19.1                        
    
  • add dr slot to compareClusterResult, enrichRestul and
    gseaResult(2021-5-21, Fri)
             Changes in version 0.99.3 (2021-05-23)                 
  • Ensured that all global variables are well-defined in the namespace.

               Changes in version 0.99.2 (2021-05-22)                 
    
  • Revised to address comments by the Bioconductor reviewer.

  • dStruct now uses the IRanges object from Bioconductor.

  • All function names follow camel case.

  • More descriptions of functions.

  • Added a test to check validity of code when running dStruct in the
    proximity_assisted mode.

               Changes in version 0.99.1 (2021-04-11)                 
    
  • Fixed errors and warnings from checks by bioc-issue-bot.

               Changes in version 0.99.0 (2021-04-07)                 
    
  • Submitted to Bioconductor

                    Changes in version 0.9.0                        
  • Added a NEWS.md file to track changes to the package.
                    Changes in version 1.5.2                        
  • Add options to collapse introns by gene and restrict introns to
    feature ranges in getFeatureRanges.
                    Changes in version 1.12                         
  • added max.overlaps and min.segment.length to provide further control
    over
    connectors. max.overlaps replaces maxoverlapsConnectors, but both can
    still
    be used for legacy purposes
                   Changes in version 1.13.2                        
  • mv ep_str_wrap to yulab.utils::str_wrap (2021-10-13, Wed)
  • adjust the order of legends for dotplot, emapplot, cnetplot and
    treeplot(2021-10-8, Fri)
  • update treeplot: add “dotplot” and “heatmap” panels for
    treeplot(2021-9-15, Wed)
  • update dotplot: enable size parameter applicable to other columns
    of
    compareClusterResult(2021-9-17, Fri)
  • enable label_format parameter for heatplot (2021-09-01, Wed)
  • add get_ggrepel_segsize function to set segment.size value for
    ggrepel(2021-08-29, Sun)
  • update ep_str_wrap (2021-08-28, Sat)
  • cnetplot now works with a named list (2021-08-23, Mon;
    clusterProfiler#362)

                     Changes in version 1.13.1                        
    
  • use aplot::plot_list instead of cowplot::plot_grid (2021-06-13, Sun
  • add color_category and color_gene parameters for
    cnetplot(2021-6-11,
    Fri)
  • Enables showCategory parameter to support character input in
    dotplot.compareClusterResult(2021-6-10, Thu)
                   Changes in version 2.17.4                        
  • Fix issue with extracting 5’ or 3’ UTRs for transcript without UTRs.

                     Changes in version 2.17.3                        
    
  • Make parameter port optional in the script to create EnsDb
    databases.

                     Changes in version 2.17.2                        
    
  • Disable ideogram plotting in vignettes.

                     Changes in version 2.17.1                        
    
  • Fix error when importing uncompressed GTF files.

             Changes in version 1.1.9 (2021-09-19)                  
  • very fast end memory-efficient BAM loading using HTSlib
    • for now reads paired-end BAM only
  • min.baseq to reduce the effect of sequencing errors

  • very fast Fisher Exact from HTSlib

  • old code removed

               Changes in version 1.1.0 (2021-05-21)                  
    
  • released at bioconductor
                    Changes in version 1.0.8                        
  • Minor bug fix in maxStepProb documentations

                      Changes in version 1.0.7                        
    
  • Exporting maxStepProb, which compute the MLE of initial and
    transition probabilities of a K-state HMM, as well as
    simulateMarkovChain, which simulates a Markov chain of length ‘n’
    given a matrix of transition probabilities

                      Changes in version 1.0.6                        
    
  • Minor bug fix in controlEM documentation

                      Changes in version 1.0.5                        
    
  • Minor bug fix in callPatterns and info function (explict import of
    S4Vectors::mcols and utils::tail).

  • Exporting expStep function, which implements the E-step of EM
    algorithm (forward-backward & Viterbi algorithm) for a K-state HMM.

                      Changes in version 1.0.4                        
    
  • Adding function callPatterns to exp[ort] combinatorial patterns (or
    posterior probabilities) associated with a given set of genomic
    regions.

  • Adding function info to print summary statistics from epigraHMM
    output. This function will print the model’s BIC, log-likelihood,
    and combinatorial patterns associated with mixture model components.

  • Adding new example dataset helas3 with ENCODE ChIP-seq data from
    broad epigenomic marks H3K27me3, H3K36me3, and EZH2.

  • Adding option to prune combinatorial patterns associated with rare
    states. See vignette for details.

  • In differential peak calling, epigraHMM now exports combinatorial
    pattern table. See vignette for details.

  • Improvement of the vignette to clarify epigraHMM’s use of
    blacklisted regions and gap tracks.

                      Changes in version 1.0.3                        
    
  • Minor updates in the NEWS file as well as the README page.

                      Changes in version 1.0.2                        
    
  • epigraHMM now exports a function called segmentGenome that segments
    a given genome (e.g. ‘mm10’) into non-overlapping genomic windows
    while considering gap tracks and blacklisted regions.

                      Changes in version 1.0.1                        
    
  • Minor fix in the package DESCRIPTION file and version numbers

                    Changes in version 1.3.1                        
                   Changes in version 1.19.1                        
  • default for typePlot: fix issue length > 1 in coercion to logical

  • fix for ggplot2 >= 3.3.4: replace guides(fill = FALSE) by guides(fill
    = ‘none’)

  • fix few notes check SummarizedExperiment + ggvis

                    Changes in version 2.1.0                        

MAJOR UPDATES

  • (2.1.1) In accordance with the deprecated caching location, upgraded
    to
    error/defunct from warning/deprecated in preparaion for removal of
    dependency next release
                   Changes in version 1.21.2                        
  • Allow writing of HaploPainter input files without a HaploPainter
    installation.

                     Changes in version 1.21.1                        
    
  • Add information on kinship-based relatedness to kinship sum test
    results.

  • Keep memory consumption constant. This allows arbitrary long
    simulation
    runs without running out of memory. Fixes issue #22. Due to the
    solution
    of that problem, histograms and densities reported by the simulation
    functions may slightly deviate from comparable former runs on the
    same
    data.

             Changes in version 1.3.1 (2021-10-13)                  
                   Changes in version 1.19.7                        
                   Changes in version 1.19.4                        
  • plotGseaTable now accepts units vector for column widths

                     Changes in version 1.19.2                        
    
  • Fixed fora() failing to run on a single pathway

  • Fixed problems random gene set generation for large k (issue #94)

  • Changed default eps to 1e-50

            Changes in version 0.99.13 (2021-08-11)                 
  • convert geom_density into geom_hist in plot_annoDistance function

              Changes in version 0.99.11 (2021-07-16)                 
    
  • add findIT_enrichWilcox function
  • delete findIT_enrichInShuffle function
  • rename findIT_enrichInAll to findIT_enrichFisher

              Changes in version 0.99.10 (2021-07-15)                 
    
  • move all shiny function in FindIT2 into InteractiveFindIT2

               Changes in version 0.99.0 (2021-06-27)                 
    
  • Submitted to Bioconductor
                    Changes in version 2.0.0                        
  • New loadFry() function, written by Dongze He with
    contributions from Steve Lianoglou and Wes Wilson.
    loadFry() helps users to import and process
    alevin-fry quantification results. Can process
    spliced, unspliced and ambiguous counts separately
    and flexibly. Has specific output formats designed
    for downstream use with scVelo or velocity analysis.
    See ?loadFry for more details.

  • Adding correlation tests: Spearman or Pearson
    correlations of a numeric covariate with the
    log counts, or with the log fold changes across
    pairs. The Spearman correlation test with counts
    was already implemented in the original SAMseq
    method as response type = “Quantitative”.
    For new functionality see ‘cor’ argument in the
    ?swish man page.

  • Adding importAllelicCounts() to facilitate importing
    Salmon quantification data against a diploid
    transcriptome. Can import either as a ‘wide’
    format or as ‘assays’. Leverages tximeta().
    For gene-level summarization, importAllelicCounts()
    can create an appropriate tx2gene table
    with the necessary a1 and a2 suffices,
    and it will automatically set txOut=FALSE, see
    ?importAllelicCounts for more details.

  • Added a ‘q’ argument to plotInfReps to change the
    intervals when making point and line plots.

  • Switched the legend of plotInfReps so that
    reference levels will now be on the bottom,
    and non-reference (e.g. treatment) on top.

                     Changes in version 1.99.18                       
    
  • Added helper functionality to importAllelicCounts,
    so it will create an appropriate tx2gene table
    with the necessary a1 and a2 suffices,
    and it will automatically set txOut=FALSE.

  • Added a ‘q’ argument to plotInfReps to change the
    intervals when making point and line plots.

  • Switched the legend of plotInfReps so that
    reference levels will now be on the bottom,
    and non-reference (e.g. treatment) on top.

  • Added loadFry() to process alevin-fry
    quantification result. Can process spliced,
    unspliced and ambiguous counts separately
    and flexibly.

                     Changes in version 1.99.15                       
    
  • Adding correlation tests: Spearman or Pearson
    correlations of a numeric covariate with the
    log counts, or with the log fold changes across
    pairs. The Spearman correlation test with counts
    was already implemented in the original SAMseq
    method as response type = “Quantitative”.
    For new functionality see ‘cor’ argument in the
    ?swish man page.

  • Adding importAllelicCounts() to facilitate importing
    Salmon quantification data against a diploid
    transcriptome. Can import either as a ‘wide’
    format or as ‘assays’. Leverages tximeta().

                      Changes in version 1.9.6                        
    
  • Specifying ties.method in matrixStats::rowRanks.

                      Changes in version 1.9.1                        
    
  • Added importAllelicCounts() with options for importing
    Salmon quantification on diploid transcriptomes.

             Changes in version 0.99.0 (2021-04-15)                 
  • Submitted to Bioconductor
                   Changes in version 2.1.24                        
  • Added UpdateMetaclusters function, removed RelabelMetaclusters,
    ReassignMetaclusters and Reordermetaclusters functions.

  • Updated CheatSheet

  • Added code from UpdateDerivedValues for metaclustersMFIs to
    UpdateFlowSOM

                     Changes in version 2.1.23                        
    
  • Added checkNames = FALSE in MetaclusterMFIs

                     Changes in version 2.1.22                        
    
  • Reordered code in UpdateDerivedValues, RelabelMetaclusters,
    ReorderMetaclusters and ReassignMetaclusters.

                     Changes in version 2.1.21                        
    
  • Added ReorderMetaclusters, to reorder the metacluster levels.

                     Changes in version 2.1.20                        
    
  • Updated PlotManualBars, Plot2DScatters and FlowSOMmary so that it
    works
    with relabeled metaclusters.

                     Changes in version 2.1.19                        
    
  • AggregateFlowFrames accepts channels and markers

  • AggregateFlowFrames now gives a warning when files do not contain the
    same
    number of channels

  • AggregateFlowFrames now gives warnings when files do not contain the
    same
    markers

  • Bugfix in AggregateFlowFrames now works when one channel is given

  • Bugfix in PlotFileScatters now works when one channel is given

  • Added silent parameter in PlotFileScatters to stop messages

  • PlotFileScatters supports channels and markers now

  • Add info to FlowSOM object: date when flowSOM object is made, FlowSOM
    verion
    and arguments given to FlowSOM call

  • Fixed bug in PlotManualBars

  • Added silent parameter in NewData. GetFeatures’ silent parameter now
    also
    surpresses message from NewData (more concrete: ReadInput)

                     Changes in version 2.1.17                        
    
  • Added ReassignMetaclusters, to rename or split metaclusters

  • Fixed issue where a lot of warnings were printed in FlowSOMmary

  • PlotFilescatters now makes filenames unique if they are not and the
    function now works with output of AggregateFlowFrames

                     Changes in version 2.1.16                        
    
  • PlotManualBars allows input of NewData function

                     Changes in version 2.1.15                        
    
  • Fixed warnings with ggtexttable in FlowSOMmary

                     Changes in version 2.1.13                        
    
  • Added RelabelMetaclusters

  • PlotFileScatters now has a parameter to change the y-axis label to
    markers
    and/or channels (yLabel)

  • Now TRUE/FALSE vector is accepted as input in GetMarkers/GetChannels

                     Changes in version 2.1.11                        
    
  • Added example to AddAnnotation

  • Added example to NClusters, NMetaclusters

  • Changed examples that used fsom to flowSOM.res

  • Added textColor and textSize to AddLabels and PlotNumbers, PlotLabels

  • PlotNumbers can plot clusters and metaclusters with parameter “level”

  • In GetFeatures, the population parameter is changed to level

  • Added GetCounts and GetPercentages to get counts or percentages
    respectively
    per cluster or metacluster

  • FlowSOMmary doesn’t crash anymore with a column with the same values
    in
    heatmap

  • Included a print function for FlowSOM class

  • Fixed bug in PlotManualBars

  • PlotMarker also accept multiple markers now

                      Changes in version 2.1.8                        
    
  • Solved issue when matrix with no column was given to the SOM function

                      Changes in version 2.1.5                        
    
  • Scale parameter in FlowSOM function defaults to FALSE.

  • FlowSOM wrapper function now returns the FlowSOM object instead of a
    list
    containing the FlowSOM object and a metaclustering

  • The metaclustering is now found as an element in the flowSOM object.
    Also the
    number of metaclusters and the MFI values are stored and can be
    accessed by
    the NMetaclusters() and GetMetaclusterMFIs() functions.

  • If you want to reuse FlowSOM objects generated by previous versions,
    you can use the UpdateFlowSOM function.

  • FlowSOM now uses nClus = 10 as default instead of maxMeta = 10

  • FlowSOM now makes use of ggplot2 for plotting. PlotFlowSOM provides
    the
    main structure, and has parameters to adapt nodeSize, view (grid, MST
    or some
    own layout matrix), … PlotStars etc build on this by adding
    additional
    layers to the ggplot object. This also allows to easily incorporate
    multiple
    plots in all layout-tools such as ggarrange, cowplot, patchwork, …

  • GetChannels/GetMarkers can now also take a FlowSOM object as input
    instead of
    a flowFrame.
    New functions:

  • To easily generate a clear summary of the model with multiple plots,
    you
    can now use the FlowSOMmary function, which creates a pdf file.

  • GetFeatures allows to map new files (internally using the NewData
    function)
    and can return cluster counts, percentages and MFI values for each
    individual
    sample.

  • PlotFileScatters can be useful to get an overview of potential batch
    effects
    before running the FlowSOM algorithm

                    Changes in version 1.1.9                        
  • Minor changes in package vignette titles.
  • Minor changes in parse_fobi() function.
  • Update all data files to FOBI 1.5 version.

fobitools 1.0.0

  • Released to Bioconductor 3.13.
                    Changes in version 2.0.0                        

MAJOR UPDATE Adding the Following Functionality:

  • Format, Library, and Testing Improvements

    o Enable processing of libraries with 1:many reagent:target assignments

    o Standardization and clarification of Annotation objects and symbol/identifier
    relationships

    o Implementation of factored quantile normalization for timecourse screens

    o Introduction of the simpleResult format and integration with associated functions

    o Conditional testing framework for quantifying and visualizing signal agreement between contrasts

  • Transition to gene set enrichment testing via Sparrow

    o Implement wrappers and provide recommendations fopr geneset enrichment testing in pooled screens

    o Implementation of GREAT-style pathway mapping for libraries with heterogenous target:gene mappings

    o Summarization tools for comparing enrichment signals across
    screens

  • New Visualization and Interpretation Tools

    o Signal Summary Barchart (Single or Multiple Contrasts)

    o Waterfall reagent/target/pathway visualization (Single Contrast)

    o Contrast comparison plots:

    • Concordance at the Top (CAT)

    • Probability Space scatter plots

    • UpSet plots with conditional overlap framework

                   Changes in version 2.23.9                        
  • Subset covariance matrix to specified samples when sample.id
    argument is passed to fitNullModel when called with an
    AnnotatedDataFrame

                     Changes in version 2.23.8                        
    
  • Added option for recessive and dominant coding to
    assocTestSingle.

                     Changes in version 2.23.7                        
    
  • Implement MatrixGenotypeReader method for pcair by writing a
    temporary GDS file.

                     Changes in version 2.23.5                        
    
  • assocTestSingle, assocTestAggregate, admixMap, and pcrelate use
    the BiocParallel package for parallel execution on blocks of
    variants.

                     Changes in version 2.23.4                        
    
  • For assocTestAggregate, the total number of genotypes in a
    single iterator element (NxM where N=number of samples and
    M=number of variants) may be >2^31.

                    Changes in version 1.6.0                        

New features

  • GeneTonic can now accept the input of clusterProfiler’s gene set
    enrichment analysis functions (gseGO and GSEA), as implemented in
    the shake_gsenrichResult() function
  • Below each plot and interactive widget, we provide a button that
    opens up a modal window where the code required to reproduce that
    output is shown as a snippet. These can be readily copied in
    extended reports or used to document the exploratory process.

Other notes

  • The manuscript about GeneTonic is now available on bioRxiv at
    www.biorxiv.org/content/10.1101/2021.05.19.444862v1 – the
    citation item has been updated accordingly
  • GeneTonic’s Shiny app now uses the latest version of bs4Dash, which
    introduced some breaking changes. Most elements should be now
    available as they were in the original implementation
                   Changes in version 1.30.0                        

NEW FEATURES

  • Register NCBI assemblies:
    • mRatBN7.2
    • UMICH_Zoey_3.1
    • Callithrix_jacchus_cj1700_1.1
    • MU-UCD_Fhet_4.1 (GCA_011125445.2)
  • Register UCSC genomes:

SIGNIFICANT USER-VISIBLE CHANGES

  • UCSC hg38 genome is now based on GRCh38.p13 instead of GRCh38.p12

  • UCSC mm10 genome is now based on GRCm38.p6 instead of GRCm38

  • seqlevelsStyle() setter now issues a warning when some seqlevels
    cannot be switched.

                  Changes in version 1.30.0                        
  • No changes in this version
                   Changes in version 1.46.0                        

SIGNIFICANT USER-VISIBLE CHANGES

  • Small update to makeTxDbFromGFF()/makeTxDbFromGRanges():
    makeTxDbFromGFF() and makeTxDbFromGRanges() now recognize and import
    features of type protein_coding_gene (or of type any offspring of
    the protein_coding_gene term) as genes. This was achieved by adding
    protein_coding_gene + its offsprings to
    GenomicFeatures:::.GENE_TYPES.
                   Changes in version 1.46.0                        
  • No changes in this version
                    Changes in version 1.2.0                        
  • [Bug Fix]
    • n argument of annotatePC was hard-coded. Now it can return
      different number of enriched pathways.
    • abs argument of annotatePC was fixed.
    • Fix wrongfully assigned variable within plotAnnotatedPCA
      function.
  • [Major]
    • drawWordcloud has a new argument droplist.
    • Argument name for plotAnnotatedPCA is changed from PCs to
      PCnum.
    • New argument studyTitle for findStudiesInCluster function.
  • [Minor]
    • Description of the package is updated.
    • If non-existing index is provided for any function, it will return
      with
      the error message.
                   Changes in version 0.99.5                        

Revisions

Revisions

Revisions

Revisions

Revisions

NEW FEATURES

  • Added a NEWS.md file to track changes to the package
  • Package template creation
                 Changes in version 2021-09-22                      
  • 0.99.1 update DESCRIPTION and NEWS files (2021-09-28, Tue)
  • 0.99.2 add documentation for row data in extdata/inst and clean up
    code (2021-09-29, Wed)
  • 0.99.3 remove some vignettes from master (build on the gh-pages
    branch) (2021-10-1, Fri)
  • 0.99.4 remove ‘stringr’ package from ‘Imports’ (2021-10-11, Mon)
  • 0.99.5 make the consensus_views compatible ggtreeExtra and add
    package description. (2021-10-21, Thu)

                     Changes in version 0.0.10                        
    
  • update default color schemes in lower part of the SeqDiff plot
    (2021-08-20, Fri)

                      Changes in version 0.0.9                        
    
  • import R4RNA to fix R check (2021-08-03, Tue)

                      Changes in version 0.0.8                        
    
  • bugfix: fix variable names error in color_scheme. (2021-07-29, Thu)
  • The migration of sequence recombination functionality from seqcombo
    package. (2021-07-20, Tue)

                      Changes in version 0.0.7                        
    
  • added gghelix() and geom_helix().(2021-04-1, Thu)
  • added option to show the fill legend.(2021-03-23, Tue)
  • added a error message to remind that “sequences must have unique
    names”.(2021-03-18, Thu)
  • added ggSeqBundle() to plot Sequence Bundles for MSAs based ggolot2
    (2021-03-18, Thu)

                      Changes in version 0.0.6                        
    
  • supports linking ggtreeExtra. (2021-01-21, Thu)
  • bugfix: reversed sequence in ‘tree + geom_facet(font)’ .
    (2021-01-21, Thu)
  • bugfix: partitioning error when the sequence starting point greater
    than 1. (2021-01-21, Thu)
  • bugfix: generates continuous x-axis labels for each panel.
    (2021-01-21, Thu)
  • supports customize colors custom_color. (2020-12-28, Mon)

                      Changes in version 0.0.5                        
    
  • added a new view called by_conservation.(2020-12-22, Tue)
  • added a new color scheme Hydrophobicity and a new parameter
    border.(2020-12-21, Mon)
  • rewrite the function facet_msa().(2020-12-03, Thu)
  • Debug: tree + geom_facet(geom_msa()) does not work.(2020-12-03,
    Thu)
  • added a new function geom_msaBar().(2020-12-03, Thu)
  • added a new parameter ignore_gaps used in consensus
    views.(2020-10-09, Fri)
  • debug in consensus views (2020-10-05, Mon)
  • added consensus views (2020-9-30, Wed)
  • added new colors LETTER and CN6 provided by ShixiangWang.issues#8

                      Changes in version 0.0.4                        
    
  • fixed warning message in msa_data.R (2020-4-26, Sun)
  • added ggplot_add methods for geom_*() (2020-4-24, Fri)
  • added a parameter seq_name in ggmsa() (2020-4-23, Thu)
  • added a new function facet_msa() –> break down the MSA (2020-4-17,
    Fri)
  • added a parameter posHighlighted in ggmsa() (2020-4-17, Fri)
  • created a new layer geom_asterisk() to optimized geom_seed()
    (2020-4-11, Sta)
  • added new functions available_colors(), available_fonts() and
    available_msa() (2020-3-30, Thu)
  • added a new function geom_seed() –> highlight the seed region in
    miRNA sequences (2020-3-27, Fri)
  • added a new function ggmotif()–> plot sequence motifs
    independently
    (2020-3-23, Tue)
  • added a Monospaced Font DroidSansMono (2020-3-23, Mon)

                      Changes in version 0.0.3                        
    
  • release of v=0.0.3 (2020-03-16, Mon)
  • added a new function geom_GC() –> plot GC content in MSA
    (2020-02-28, Fri)
  • added a new function geom_seqlogo() –> plot plot sequence motifs
    in
    MSA (2020-02-14, Fri)
  • used a proportional scaling algorithm (2020-01-08, Wed)

                      Changes in version 0.0.2                        
    
  • support plot sequence logo (2019-12-25, Wed)
  • added three fonts:helvetical, times_new_roman, mono (2019-12-21,
    Sta)
  • added three fonts:serif_font, Montserrat_font, roboto_font
    (2019-12-17, Tue)
  • added internal outline polygons (2019-12-15, Sun)
  • bug fixed of tidy_msa
  • import seqmagick for parsing fasta
  • tidy_msa for converting msa file/object to tidy data frame
    (2019-12-09, Mon)

                      Changes in version 0.0.1                        
    
  • initial CRAN release (2019-10-17, Thu)
  • removed from CRAN on 2021-08-17
             Changes in version 0.99.0 (2021-08-08)                 
  • version for submission to Bioconductor
                    Changes in version 3.1.6                        
  • geom_cladelab now supports extend parameter as in geom_cladelabel
    (2021-10-14, Thu, @xiangpin, #446)
  • geom_hilight supports fill linear gradient colour and round rect
    background (2021-10-11, Mon; @xiangpin, #449, #444)
  • work with negative edge lengths (hclust may generate negative tree
    heights) (2021-09-29, Wed; @xiangpin, #441, #445)

                      Changes in version 3.1.5                        
    
  • ggdensitree with align.tips=TRUE sets max x to 0 (2021-09-26, Sun;
    @brj1, #437, #439)
  • custom column headers for gheatmap (2021-09-15, Wed,
    @matt-sd-watson, #434)
  • bug fixed of nudge_x parameter in geom_segment2 (2021-09-03, Fri;
    @xiangpin, #433)

                      Changes in version 3.1.4                        
    
  • introduce align parameter in geom_hilight (2021-08-30, Mon;
    @xiangpin, #431)
  • the data parameter in geom_facet now accepts function as input
    (2021-08-22, Sun; @xiangpin, #430)
  • import ggfun and yulab.utils (2021-08-20, Fri)
  • allow using options(layout.radial.linetype) to set linetype of
    radial layout (either ‘strainght’ or ‘curved’) (2021-08-13, Fri;
    @xiangpin, #427)

                      Changes in version 3.1.3                        
    
  • data argument in geom_tiplab and position argument in geom_tree
    (2021-08-10, Tue; #426, @xiangpin)
  • geom_hilight and geom_cladelab supports function as input data
    (2021-07-28, Wed; #421, @xiangpin)
  • td_mutate for mutating tree data
  • geom_tiplab supports fontface aesthetic (2021-07-06, Tue;
    @xiangpin)

                      Changes in version 3.1.2                        
    
  • calculate branch mid point for unrooted layout tree (2021-06-11,
    Fri)
  • branch.y and branch.x
  • geom_range supports aes mapping (2021-06-04, Fri)

                      Changes in version 3.1.1                        
    
  • bug fixed in geom_range (2021-06-01, Tue)
  • github.com/YuLab-SMU/ggtree/pull/410
  • now geom_nodelab has a node=”internal” parameter. (2021-05-31, Mon)
  • if node = “external”, it equivalent to `geom_tiplab
  • if node = “all”, it equivalent to list(geom_tiplab(),
    geom_nodelab())
                    Changes in version 1.3.6                        
  • fix the issue of gridlines when some data is removed. (2021-08-25,
    Wed)

                      Changes in version 1.3.5                        
    
  • update citation of ggtreeExtra (2021-08-25, Wed).

                      Changes in version 1.3.4                        
    
  • fix the compute_aes to better compatible with ggplot2 (>=3.3.4)
    (2021-08-09, Mon)
  • The ggplot2 (>=3.3.4) introduced computed_mapping.

                      Changes in version 1.3.3                        
    
  • update reference. (2021-06-08, Tue)
  • fix vector logical check. (201-06-11, Fri)
  • c(TRUE, TRUE) && c(TRUE, TRUE) is not allowed in devel
    environment of bioconductor

                      Changes in version 1.3.1                        
    
  • data argument of geom_fruit support function input. (2021-05-20,
    Thu)
  • the argument of axis.params and grid.params can be assigned by
    intermediate variables. (2021-05-26, Wed)
  • github.com/YuLab-SMU/ggtreeExtra/issues/9

                      Changes in version 1.3.0                        
    
  • new version release, and bump new devel version (1.3.0).
    (2021-05-20, Thu)
                     Changes in version 1.5                         
  • Choose a more reasonable scale for global overdispersion estimate

  • Make code more robust accidental internal NA’s

  • Add fallback mechanism in case the Fisher scoring fails to converge.
    Instead of returing NA, try again using the BFGS algorithm.

  • Better error message if the design contains NA’s

                   Changes in version 1.13.1                        

USER-LEVEL CHANGES

  • update GO-graph (version 01-May-2021)
                   Changes in version 2.19.1                        
  • TCSS method (@qibaiqi, #35; 2021-08-02, Mon)

  • GOSemSim 2.18.0

  • Bioconductor 3.13 release

                    Changes in version 1.8.0                        
                    Changes in version 1.56                         

SIGNIFICANT USER-VISIBLE CHANGES

                    Changes in version 1.50                         

BUG FIXES

  • Bugfix for github.com/rcastelo/GSVA/issues/54 to force
    filtering genes with constant expression behaving the same regardless
    of the delayed or non-delayed nature of the data container.
            Changes in version 1.22.0
  • No changes in this version
             Changes in version 1.27.1 (2021-07-28)                 
             Changes in version 1.1.3 (2021-07-06)                  
  • Modify the plotting functions.

               Changes in version 1.1.2 (2021-06-14)                  
    
  • Add APIs for Seurat pipeline and igraph pipeline.

               Changes in version 1.1.1 (2021-05-27)                  
    
  • Modify the package manual.

               Changes in version 1.1.0 (2021-05-20)                  
    
  • The development version 1.1.0 is available in Bioconductor.

                   Changes in version 1.27.1                        
  • Suggest ‘markdown’ package in DESCRIPTION and utilize hg19 as default
    freeze where applicable.
                   Changes in version 1.30.0                        
  • add the support of Intel AVX-512VPOPCNTDQ intrinsics (faster than
    AVX512BW)
             Changes in version 1.7.6 (2020-10-13)                  
  • Trigger bioc build

               Changes in version 1.7.5 (2020-10-08)                  
    
  • Update R version dependency from 3.6 to 4.1

               Changes in version 1.7.4 (2020-10-08)                  
    
  • Fix a typo

  • Add citation file

               Changes in version 1.7.3 (2020-10-07)                  
    
  • Prepare for release

               Changes in version 1.7.2 (2020-10-07)                  
    
  • Fix warnings in unit tests

               Changes in version 1.7.1 (2020-10-07)                  
    
  • Update the man files

                   Changes in version 1.29.1                        
  • Suggest ‘markdown’ package in DESCRIPTION
                    Changes in version 1.35                         

Changes in version 1.35.1

Changes in version 1.35.0

                    Changes in version 1.2.1                        
            Changes in version 0.99.17 (2021-09-16)                 
                    Changes in version 1.9.1                        
                   Changes in version 1.18.0                        

Bug fixes

  • Fixed the unexpected behaviour when decorating the signature
    heatmap
    with colData elements

Other notes

  • Some alignments of the UI elements in the ideal() app, to harmonize
    the content of the page
  • Updated the icons in the user interface to match recent changes in
    the names from FontAwesome
             Changes in version 1.7.24 (2021-10-14)                 
  • minor model update: top level hyperpriors on alpha gamma par.
    means not needed anymore. Compare inst/extdata/zibb.stan vs.
    inst/extdata/zibb_original.stan
             Changes in version 0.99.9 (2021-10-22)                 
  • Removed certain unit tests for 64-bit windows

               Changes in version 0.99.8 (2021-10-11)                 
    
  • Added patch detection method

               Changes in version 0.99.7 (2021-10-10)                 
    
  • Added all unit tests

  • Fixed read_steinbock x/y axis defaults

               Changes in version 0.99.0 (2021-09-14)                 
    
  • Bioconductor submission

               Changes in version 0.3.12 (2021-09-01)                 
    
  • clean up for Bioconductor submission

               Changes in version 0.3.11 (2021-08-19)                 
    
  • Added flip_x, flip_y argument for plotSpatial function

  • readSCEfromTXT does not require spot names anymore

  • knn graph construction can be pruned by distance

  • added

               Changes in version 0.3.10 (2021-08-18)                 
    
  • Added countInteractions function

  • Added testInteractions function

               Changes in version 0.3.9 (2021-07-29)                  
    
  • Added buildSpatialGraph function

  • Added plotSpatial function

  • Added aggregateNeighbors function

               Changes in version 0.3.8 (2021-06-30)                  
    
  • Adjusted default parameters for read_steinbock function

  • Added updated test data

               Changes in version 0.3.7 (2021-06-14)                  
    
  • added read_cpout function, docs and tests

               Changes in version 0.3.6 (2021-06-04)                  
    
  • added read_steinbock function, docs and tests

               Changes in version 0.3.5 (2021-05-20)                  
    
  • unit tests and docs for filterPixels

               Changes in version 0.3.4 (2021-05-18)                  
    
  • added readImagefromTXT function and tests

               Changes in version 0.3.3 (2021-05-17)                  
    
  • unit tests for binAcrossPixels

               Changes in version 0.3.2 (2021-05-16)                  
    
  • adjusted plotSpotHeatmap function and unit test

               Changes in version 0.3.1 (2021-05-15)                  
    
  • readSCEfromTXT accepts list and path

               Changes in version 0.3.0 (2021-05-07)                  
    
  • Added helper functions for spillover correction

  • Removed redundant functions

               Changes in version 0.2.0 (2019-11-28)                  
    
  • The functions calculateSummary, plotCellCounts, and plotDist have
    been added

               Changes in version 0.1.0 (2019-09-17)                  
    
  • initial commit

                   Changes in version 1.25.2                        
  • CHANGES
  • CHANGES
    • bugfix im subset.immunoMeta-object
             Changes in version 1.1.1 (2021-08-09)                  
  • Resolved error due to MHC reference list reading.
             Changes in version 1.8.1 (2020-08-16)                  
                    Changes in version 1.1.4                        
  • For the three div blocks of heatmap widgets, now display:table-cell
    is used so that
    the positions of divs won’t change when changing the size of the
    browser window.

  • Add a new vignette “Share interactive heatmaps to collaborators”.

                      Changes in version 1.1.3                        
    
  • fontawesome is directly from the fontawesome package.

  • also inherit row_names_gp and column_names_gp from the complete
    heatmap

  • content of js and css for specific heatmap is directly add to html
    instead of
    containing as files

                      Changes in version 1.1.2                        
    
  • Add save argument in htShiny().

                      Changes in version 1.1.1                        
    
  • add new argument sub_heatmap_cell_fun and sub_heatmap_layer_fun
    to only set cell_fun
    or layer_fun for sub-heatmaps.

             Changes in version 2.0.0 (2021-10-20)                  
  • Added upload of up to 6 datasets that can be analyzed in parallel
  • Added CellChat and ICELLNET as supported tools
  • Added multiple conditions comparison in data-driven analysis
  • Added significant functional terms in multiple conditions
  • Added output folder and file download in automatically generated
    folders
  • Added weighting for interactions
  • Added Network in gene-verse
  • Updated About page
                    Changes in version 0.99                         

NEW FEATURES

                   Changes in version 2.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

  • Replace dim(), nrow(), and ncol() methods for DataFrameList objects
    with
    dims(), nrows(), and ncols() methods.

DEPRECATED AND DEFUNCT

  • Deprecate dim(), nrow(), and ncol() methods for DataFrameList objects
    in favor of the new dims(), nrows(), and ncols() methods.
             Changes in version 1.3.9 (2021-10-25)                  

FIXES

NEW

  • Added new feature iss_source()

FIXES

NEW

  • Added new feature purity_filter()

FIXES

MAJOR CHANGES

  • Reworked is_sharing() function, detailed usage in vignette
    vignette(“sharing_analyses”, package = “ISAnalytics”)

NEW

FIXES/MINOR UPDATES

MAJOR CHANGES

  • Completely reworked interactive HTML report system, for details
    take
    a look at the new vignette vignette(“report_system”, package =
    “ISAnalytics”)
  • Old ISAnalytics.widgets option has been replaced by
    ISAnalytics.reports
  • In remove_collisions(), removed arguments seq_count_col,
    max_rows_reports and save_widget_path, added arguments quant_cols
    and report_path (see documentation for details)

MINOR CHANGES

  • import_single_Vispa2Matrix() now allows keeping additional
    non-standard columns
  • compute_near_integrations() is now faster on bigger data sets
  • Changed default values for arguments columns and key in
    compute_abundance()
  • compute_near_integrations() now produces only re-calibration map in
    *.tsv format
  • CIS_grubbs() now supports calculations for each group specified in
    argument by
  • In sample_statistics() now there is the option to include the
    calculation of distinct integration sites for each group (if
    mandatory vars are present)

NEW FUNCTIONALITY

  • Added new plotting function circos_genomic_density()

FIXES

  • Fixed minor issue with NA values in alluvial plots

DEPRECATIONS

  • import_parallel_Vispa2Matrices_interactive() and
    import_parallel_Vispa2Matrices_auto() are officially deprecated in
    favor of import_parallel_Vispa2Matrices()

OTHER

FIXES

NEW FUNCTIONALITY

  • is_sharing computes the sharing of IS between groups
  • sharing_heatmap allows visualization of sharing data through
    heatmaps
  • integration_alluvial_plot allows visualization of integration sites
    distribution in groups over time.
  • top_abund_tableGrob can be used in combination with the previous
    function or by itself to obtain a summary of top abundant
    integrations as an R graphic (tableGrob) object that can be combined
    with plots.

MINOR UPDATES

  • Added more default stats functions to default_stats
  • Added optional automatic conversion of time points in months and
    years when importing association file
  • Minor fixes in generate_Vispa2_launch_AF
                    Changes in version 2.5.3                        
                    Changes in version 1.5.2                        
            Changes in version 1.15.02 (2021-09-14)                 
  • Update type: minor.

  • Various error message updates

              Changes in version 1.15.01 (2021-09-01)                 
    
  • Update type: minor.

  • Version bump due to Bioconductor release.

  • preFilter() now applies the gene expression cutoff to both conditions
    instead of the overall average.

  • analyzePFAM() was updated to reflect recent updates to the tidyverse
    read_fwf function. It furhtermore now better distinguishes tap
    seperated and fixed with files.

                   Changes in version 1.21.1                        

FIX

                   Changes in version 1.27.2                        
  • fix in evaluatePrediction() (avoid length>1 logical condition)

                     Changes in version 1.27.1                        
    
  • fix to avoid warnings arising from compiled code

  • fix in kebabsDemo() to avoid build warnings; executing this function
    now does
    not have any side effects anymore (previously, data objects were
    loaded into the
    global workspace)

                     Changes in version 1.27.0                        
    
  • new branch for Bioconductor 3.14 devel

                   Changes in version 3.50.0                        
  • Improve help pages for fry() and barcodeplot().

  • Revise Section 18.1.10 of User’s Guide so that coloring of X
    and Y genes is consistent between plots.

  • Fix bug in the MDS class method of plotMDS() (introduced in the
    previous release) when new dim.plot values are set.

  • Fix bug in read.idat() when annotation contains NA values.

                   Changes in version 1.19.2                        
  • Eliminated some duplication resulting from relict “trimmed_databases”
    directory

                     Changes in version 1.18.1                        
    
  • Updated authors and maintainers

  • Formalized support for new lipid classes including bile salts, wax
    esters,
    quinones, etc.

                   Changes in version 1.10.1                        

NEW FEATURES

  • (v 1.10.1) add ‘/attrs’ to metadata, if present

BUG FIXES

  • (v 1.10.1) don’t drop all metadata when ReducedDims is not present
                    Changes in version 2.4.0                        
  • LRBase.XXX.eg.db-type annotation packages for organisms were
    deprecated.

  • The distribution of each SQLite file has been changed to the
    AnnotationHub-style.

  • By using LRBaseDbi, we can convert SQLite files acquired by the
    AnnotationHub’s query function into LRBase objects, which can then be
    used for analysis using LRBase.XXX.eg.db as before.

  • makeLRBasePackage function was deprecated.

  • .loadLRBaseDbiPkg was deprecated.

             Changes in version 0.99.0 (2021-05-27)                 
  • Submitted to Bioconductor
                    Changes in version 1.7.1                        
                    Changes in version 3.14                         

NEW FUNCTIONS

  • sampleSwaps Given a list BAM files, the function genotypes known
    SNPs and identifies potentially related samples.

BUG FIXES

  • Return mutCountMatrix output as a matrix Issue: 769

ENHANCEMENTS

  • Added showPct argument to oncoplot. Issue: Issue: 771
  • Silently return sample order from oncoplot and coOncoplots Issue:
    771
                    Changes in version 3.13                         
  • added feature-label output on May 10, 2021

                      Changes in version 3.12                         
    
  • added feature-label output on April 27, 2021

  • added cutoff value on March 06, 2021

                    Changes in version 1.5.4                        
             Changes in version 1.1.2 (2021-09-06)                  
  • take sample IDs for shinyQC from colnames(se)

  • take feature IDs for shinyQC from rownames(se)

  • fix error in report.Rmd (change input for
    create_boxplot to se)

               Changes in version 1.1.1 (2021-08-27)                  
    
  • fix bug in biocrates and maxQuant function

             Changes in version 1.19.1 (2021-10-20)                 

BUG FIXES

  • Fix error in ‘cbind()’ on two ‘matter_vec’ objects
                    Changes in version 1.3.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  • Make install_megadepth more transparent for users. Interactive
    sessions will now prompt users to agree to the install Megadepth at
    the printed locations.
                    Changes in version 1.1.3                        
  • fixed a bug in runTomTom where setting norc = TRUE failed on data
    import

                      Changes in version 1.1.1                        
    
  • runFimo now returns NULL and prints a message when text = FALSE and
    FIMO detects no matches instead of throwing a cryptic error message

                   Changes in version 1.30.0                        
  • MeSH-related packages (MeSH.XXX.eg.db, MeSH.db, MeSH.AOR.db, and
    MeSH.PCR.db) were deprecated.

  • The distribution of each SQLite file has been changed to the
    AnnotationHub-style.

  • By using MeSHDbi, we can convert SQLite files acquired by the
    AnnotationHub’s query function into MeSH objects, which can then be
    used for analysis using MeSH-related packages as before.

  • makeGeneMeSHPackage was deprecated.

  • .loadMeSHDbiPkg was deprecated.

                   Changes in version 1.19.3                        
  • cache mesh db and table (2021-09-01, Wed)

                     Changes in version 1.19.2                        
    
  • import yulab.utils (2021-8-19, Thu)

                     Changes in version 1.19.1                        
    
  • remove MeSH.db package and use AnnotationHub to get MeSHDb
    databases
    (2021-8-13, Fri)

                    Changes in version 2.0.0                        
  • Specification changed as “AnnotationHub-style”

  • Dependencies of MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSH.Hsa.eg.db,
    MeSH.Aca.eg.db, MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db were removed

  • Vignette changed for the specification change

  • All datasets removed

                    Changes in version 1.3.2                        

Changes to labelRows

  • new resolveConflicts + rtOrder argument added for automated
    resolution of
    conflicting feature pair alignment fows in combinedTable, with
    embedded
    C function (resolveRows.c)

  • new argument rtOrder paired with resolveConflicts determines if RT
    order
    consistency is expected when resolving alignment conflicts

  • duplicate column names for {labels, subgroup, alt} removed and no
    longer
    allowed in resulting combinedTable

Changes to metabCombiner

  • new check for metabCombiner object inputs: labelRows must be called
    before
    aligning a metabCombiner object with a new dataset

  • resolveConflicts method applied to metabCombiner object to eliminate
    conflicting alignments/ attain 1-1 matches for all features

  • new rtOrder argument controlling resolveConflicts similar to above

                      Changes in version 1.3.1                        
    

Changes to fit_gam()/ fit_loess

  • messages changed from using cat() to using message()

Changes to metabCombiner() & combinedTable / featdata slots

  • rowID column now the first column in both tables instead of having
    this
    information be the row names

Changes to calcScores() / evaluateParams() / labelRows

  • updated to reflect above changes to keep rowID identical between
    combinedTable & featdata

Changes to write2file

  • combinedTable & featdata merged by rowID column when metabCombiner
    objects
    used as input
                     Changes in version 1.1                         

MetaboCoreUtils 1.1.1

  • Add correctRindex function.
  • Add isotopologue function to group isotopologues in MS spectra.
             Changes in version 1.5.1 (2021-06-14)                  

NEW FEATURES

BUG FIXES

                   Changes in version 0.99.27                       
  • New package in Bioconductor 3.14 release
             Changes in version 1.11.5 (2021-10-12)                 
  • add assays in structural based on columns in transformations that are
    defined by the var argument in structural, adjacency matrices of type
    will be stored in the AdjacencyMatrix object defined in the columns
    of
    transformation

  • implement structural that it can also calculate mass differences of 0
    for
    undirected networks

               Changes in version 1.11.4 (2021-09-09)                 
    
  • shift calculation of as.data.frame(am) in mz_summary

  • several fixes of typos in the comments and vignette

  • fix rtCorrection function

               Changes in version 1.11.3 (2021-08-30)                 
    
  • change calculation of mass differences, use the differences between
    (M_2+ppm)-(M_1-ppm) and (M_2-ppm)-(M_1+ppm) instead of
    (M_1-ppm)-(M_1) and
    (M_2+ppm)-(M_1) for querying against the list of transformations

               Changes in version 1.11.2 (2021-08-30)                 
    
  • change error message in test_combine

              Changes in version 1.1 (2021-06-04)                   
  • split transformCounts into transformSamples and transformFeatures

  • added log_modulo_skewness as a diversity index

  • added functions for summarizing dominant taxa information

  • added wrapper for adding dominant taxa information to colData

  • added specialized subsetting function for subsetting by prevalence
    (subsetByPrevalentTaxa/subsetByRareTaxa)

  • added mapTaxonomy

  • added estimateDivergence

  • bugfix: makePhyloseqFromTreeSummarizedExperiment checks now for
    rowTree be compatible

  • bugfix: meltAssay supports Matrix types

  • bugfix: meltAssay is able to include rowData also when there are
    duplicated rownames

  • added subsampleCounts for Subsampling/Rarefying data

             Changes in version 0.99.0 (2021-09-29)                 
                     Changes in version 1.1                         
  • Added plotAbundanceDensity (2021-06-23)
             Changes in version 2.1.2 (2020-07-01)                  
  • Core heatmap labeling improved

  • aggregate_top_taxa deprecated

  • bimodality and potential_analysis functions fixed

               Changes in version 2.1.1 (2020-04-06)                  
    
  • Added overlap function

               Changes in version 1.14.1 (2021-09-29)                 
    
  • Removed categorical method from associate function

             Changes in version 0.99.0 (2021-09-01)                 
  • Submitted to Bioconductor
                   Changes in version 0.99.0                        
  • Added a NEWS.md file to track changes to the package.
                    Changes in version 1.5.9                        
  • add include.rownames to control whether consider the OTU as
    taxonomy
    feature table in diff_analysis and get_alltaxadf or tip labels in
    as.treedata. (2021-10-19, Tue)
  • fix rename bug, rename the taxonomy names can work now.
    (2021-10-12,
    Tue)
  • introduce trimSample in mp_rrarefy to check whether to remove the
    samples that do not have enough abundance. (2021-10-11, Mon)
  • update MPSE to allow assays supporting data.frame or DFrame class.
    (2021-10-08, Fri)
  • update mp_plot_ord to suppress the message of the third depend
    package. (2021-10-08, Fri)

                      Changes in version 1.5.8                        
    
  • fix the bug of AsIs list class in unnest for the tidyr (>= 1.1.4).
    (2021-10-01, Fri)
  • add mp_aggregate function. (2021-09-26, Sun)

                      Changes in version 1.5.7                        
    
  • fix bug of mp_plot_upset. (2021-09-10, Fri)
  • update the mp_plot_ord. (2021-09-13, Mon)

                      Changes in version 1.5.6                        
    
  • convert the type of first element of assays to matrix to compatible
    with DESeqDataSet of DESeq2, test_differential_abundance of
    tidybulk. (2021-09-09, Thu)
  • update show and print for format output of MPSE class. (2021-09-08,
    Wed)
  • update mp_cal_abundance use new tidytree. (2021-09-07, Tue)
  • introduce include.lowest parameter in mp_filter_taxa. (2021-09-07,
    Tue)

                      Changes in version 1.5.5                        
    
  • update mp_plot_ord to display the bioplot for result of cca, rda
    and
    envfit. (2021-09-06, Mon)
  • update the vignettes of MicrobiotaProcess. (2021-09-04, Sat)
  • return updated MPSE object after the mp_diff_analysis is done with
    action=”add”. (2021-08-31, Fri)
  • then the taxtree and otutree with the result of different
    analysis can be extracted with mp_extract_tree.
  • fix issue print for one line of MPSE and update mp_plot_ord to
    display the side boxplot. (2021-08-31, Tue)
  • add mp_plot_ord for MPSE or tbl_mpse object after one of
    mp_cal_pca,
    mp_cal_pcoa, mp_cal_rda, mp_cal_nmds, mp_cal_rda, mp_cal_cca,
    mp_cal_dca or mp_envfit has been run with action=’add’. (2021-08-30,
    Mon)
  • add mp_plot_dist for MPSE or tbl_mpse object after mp_cal_dist is
    performed with action=”add”. (2021-08-28, Sat)
  • add mp_plot_abundance, mp_plot_alpha, mp_plot_rarecurve,
    mp_plot_venn, mp_plot_upset for MPSE after the corresponding
    mp_cal_abundance, mp_cal_alpha, mp_cal_rarecurve, mp_cal_venn,
    mp_cal_upset are performed with action=”add”. (2021-08-27, Fri)
  • fix the issue when the rowname or colnames of SummarizedExperiment
    is NULL for as.MPSE. (2021-08-26, Thu)

                      Changes in version 1.5.4                        
    
  • fix the rownames of assays and colnames of colData to identical for
    SummarizedExperiment(1.23.3). (2021-08-26, Thu)
  • add mp_extract_refseq for MPSE object. (2021-08-25, Wed)
  • update as.MPSE for SummarizedExperiment object. (2021-08-24, Tue)
  • add mp_filter_taxa to drop the taxa that low abundance and low
    occurrences. (2021-08-24, Tue)
  • add colData<- and left_join for MPSE. (2021-08-23, Mon)
  • fix mutate for MPSE object.
  • don’t import the parse_taxonomy_greengenes and parse_taxonomy_qiime
    from phyloseq. (2021-08-17, Tue)
  • add as.MPSE for TreeSummarizedExperiment class. (2021-08-17, Tue)
  • add mp_import_metaphlan to parsing the output of MetaPhlAn.
    (2021-08-12, Thu)
  • add treefile argument to import the tree of MetaPhlAn3
    (mpa_v30_CHOCOPhlAn_201901_species_tree.nwk) (2021-08-13, Fri)
  • update the print of MPSE object via pillar package. (2021-08-06,
    Fri)
  • update mp_extract_dist by introducing .group argument to return a
    tbl_df for visualization. (2021-08-04, Wed)
  • add taxatree, taxatree<-, otutree, otutree<-, refseq, refseq<- for
    MPSE. (2021-08-04, Wed)
  • add mp_extract_rarecurve to extract the result of mp_cal_rarecurve
    from MPSE or tbl_mpse object. (2021-08-04, Wed)
  • add mp_stat_taxa to count the number and total number taxa for each
    sample at different taxonomy levels (Kingdom, Phylum, Class, Order,
    Family, Genus, Species, OTU). (2021-08-03, Tue)

                      Changes in version 1.5.3                        
    
  • rename mp_extract_abundance to mp_extract_assays from MPSE or
    tbl_mpse. (2021-07-31, Sat)
  • update the method to save the result of mp_cal_clust by introducing
    action argument. (2021-07-29, Thu).
  • update as.phyloseq for MPSE or tbl_mpse object. (2021-07-28, Wed)
  • add mp_diff_analysis for MPSE or tbl_mpse object. (2021-07-27, Tue)
  • add dr_extract for the visualization of the result of ordination.
    (2021-07-26, Mon)
  • comment out the function for phyloseq and add rd of the function
    for
    MPSE or tbl_mpse. (2021-07-24, Sat)
  • update the function to parsing the result of rda, cca, envfit.
    (2021-07-23, Fri)
  • add tidydr to convert the result of reduce dimension to tbl_df
  • such pca, pcoa, nmds, rda, cca. (2021-07-22, Thu)
  • optimize the print for MPSE. (2021-07-22, Thu)

                      Changes in version 1.5.2                        
    
  • add mp_mantel and mp_mrpp for MPSE or tbl_mpse object. (2021-07-19,
    Mon)

  • add mp_envfit and update mp_cal_dist to support the distance
    calculation with continuous environment factors and rename
    mp_cal_adonis to mp_adonis, mp_cal_anosim to mp_anosim. (2021-07-17,
    Sat)

  • add mp_cal_rda, mp_cal_cca, mp_cal_adonis and mp_cal_anosim for
    MPSE
    or tbl_mpse object. (2021-07-16, Fri)

  • add mp_cal_dca, mp_cal_nmds and mp_extract_internal_attr.
    (2021-07-15, Thu)

  • add mp_cal_pca, mp_cal_pcoa and mp_extract_abundance. (2021-07-14,
    Wed)

  • add mp_cal_clust to perform the hierarchical cluster analysis of
    samples and mp_extract_dist to extract the dist object from MPSE
    object or tbl_mpse object. (2021-07-13, Thu)

  • add mp_cal_dist to calculate the distance between samples with MPSE
    or tbl_mpse object. (2021-07-12, Mon)

  • add mp_extract_sample, mp_extract_taxonomy, mp_extract_feature to
    extract the sample, taxonomy and feature (OTU) information and
    return tbl_df or data.frame. (2021-07-09, Fri)

  • add mp_cal_venn to build the input for venn plot (2021-07-09, Fri)

  • mp_cal_rarecurve add action argument to control whether the result
    will be added to MPSE and tbl_mpse or return directly. (2021-07-08,
    Thu)

  • add mp_cal_upset to get the input of ggupset. (2021-07-08, Thu)

  • add mp_extract_tree to extract the otutree or taxatree from MPSE or
    tbl_mpse object. (2021-07-07, Wed)

  • add pull and slice to support the MPSE object. (2021-07-06, Tue)

  • add mp_cal_rarecurve to calculate the rarecurve of each sample with
    MPSE or tbl_mpse. (2021-07-06, Tue)

  • add mp_cal_abundance to calculate the relative abundance of each
    taxonomy class with MPSE or tbl_mpse. (2021-07-05, Mon)

  • add mp_decostand provided several standardization methods for MPSE,
    tbl_mpse and grouped_df_mpse. (2021-07-04, Sun)

  • add mp_import_qiime to parse the output of qiime old version.
    (2021-07-03, Sat)

  • add taxatree slot to MPSE. (2021-06-30, Wed)

  • add mp_cal_alpha function for MPSE or mpse object. (2021-07-01,
    Thu)

  • add rownames<- to support renaming the names of feature.
    (2021-07-01, Thu)

  • add mp_import_qiime2 and mp_import_dada2 to parse the output of
    dada2 or qiime2 and return MPSE object. (2021-07-02, Fri)

  • update print information for MPSE, tbl_mpse and grouped_df_mpse.
    (2021-06-29, Tue)

  • add [ to the accessors of MPSE. (2021-06-29, Tue)

  • use MPSE object. (2021-06-28, Mon)

  • add as.MPSE to convert phyloseq or tbl_mpse to MPSE class.
  • Formatted output.

  • tidy framework for MPSE object.
  • as_tibble to convert MPSE and phyloseq to tbl_mpse. (2021-06-28,
    Mon)
  • filter to subset a data frame from tbl_mpse. (2021-06-28, Mon)
  • group_by to do some data operations on groups for tbl_mpse.
    (2021-06-28, Mon)
  • arrange to order the rows of a data frame for tbl_mpse.
    (2021-06-28, Mon)
  • mutate to adds new variables and preserves existing ones for
    tbl_mpse. (2021-06-28, Mon)
  • select to select variables in tbl_mpse. (2021-06-28, Mon)
  • distinct to select only unique/distinct rows in tbl_mpse.
    (2021-06-28, Mon)
  • rename to rename the variable names in tbl_mpse. (2021-06-28,
    Mon)
  • nest to create a list-column of tbl_mpse, it will convert
    tbl_mpse to tbl_mpse_nest. (2021-06-28, Mon)
  • unnest to convert the tbl_mpse_nest to tbl_mpse. (2021-06-28,
    Mon)
  • as.treedata to convert tbl_mpse to treedata, then we can explore
    the data with treedata.
  • add tiplevel argument to control whether use OTU as tip
    label, default is OTU. (2021-06-28, Mon)
  • left_join to mutate joins based the left tbl_mpse structure.
    (2021-06-28, Mon)
  • changed clustplotClass to treedata. (2021-06-28, Tue)
  • add mp_rrarefy method to rarefy species richness. (2021-06-29, Tue)
  • it supports MPSE, tbl_mpse, grouped_df_mpse object via wrapping
    vegan::rrarefy.
  • update as.MPSE and as.treedata for grouped_df_mpse object.
    (2021-06-29, Tue)
    – This feature is useful to explore the
    microbiome data in taxa tree.
    This feature has been replaced by
    the taxatree slot

                      Changes in version 1.5.1                        
    
  • add ellipse_linewd and ellipse_lty in ggordpoint to control the
    width and line type of ellipse line. (2021-05-24, Mon)
  • fixed the regular expression match for the internal function to
    print the results of diff_analysis. (2021-06-06, Sun)
  • add filter function to filter the result of diff_analysis.
    (2021-06-07, Mon)
  • more accessor function for result of diff_analysis. (2021-06-07,
    Mon)
  • head
  • tail
  • [
  • [[]]
  • $
  • dim
  • add get_NRI_NTI to calculate the NRI and NTI. (2021-06-08, Tue)
                    Changes in version 1.1.0                        
  • Bioconductor release!

                     Changes in version 1.0.13                        
    
  • adds new HLA-KIR interaction A03_A11_KIR3DL2 defined as (A03 | A11)
    & KIR3DL2.

                     Changes in version 1.0.12                        
    
  • fixes bug causing MiDAS subsetting to break omnibus testing.

                     Changes in version 1.0.11                        
    
  • runMiDAS inheritance_model argument is no longer by defaut
    ‘additive’. Now it is required to specify desired inheritance model,
    when appplicable.

                     Changes in version 1.0.10                        
    
  • fix bug causing Bw6 groups to be counted twice in hla_NK_lingads
    experiment.

                      Changes in version 1.0.9                        
    
  • fix bug causing runMiDAS errors when statistical model evaluated
    with a warrning.

                      Changes in version 1.0.8                        
    
  • fixed bug causing filterByVariables and filterByFrequency to strip
    omnibus groups from target experiment.

                      Changes in version 1.0.7                        
    
  • fixed bug causing HWETest filtration to strip omnibus groups from
    target experiment

                      Changes in version 1.0.6                        
    
  • removed unused expression dictionaries

                      Changes in version 1.0.4                        
    
  • In frequency calculations the “NA”s were counted as non-carriers,
    this has been changed such that “NA” samples are now omitted.

                      Changes in version 1.0.3                        
    
  • warnings and errors occuring upon model evaluation are now
    summarized into more readable form

                      Changes in version 1.0.2                        
    
  • fixed problem vignettes index entry values, preventing vignettes
    from being build

                      Changes in version 1.0.1                        
    
  • fixed bug in summariseAAPos, where argument specifying AA position
    didn’t consider AA position numbering starting from negative
    positions
  • frequencies in getFrequencies output are no longer formatted as
    percentages
  • kableResults scroll box height can now be adjusted
  • omnibus result columns: dof, residue were renamed to df, residues
  • missing Bw6 references were added to allele_HLA_Bw dictionary
  • new inheritance model has been added the overdominance
             Changes in version 1.1.0 (2021-10-12)                  
  • Fix bug in testNhoods to use user-specific reduced dimensions
  • Vignettes now include set rownames() to avoid confusion
  • Numerous doc-string typo fixes
                    Changes in version 1.39                         
  • v1.39.1 Initial support for the Allergy and Asthma array.

  • v1.39.2 More support for the Allergy and Asthma array.

  • v1.39.3 Bug fix that prevented R CMD build from working.

             Changes in version 1.1.5 (2021-08-24)                  
  • Updated citation

               Changes in version 1.1.3 (2021-05-27)                  
    
  • Added new option for model_type, one_dimensional

  • Added new filtering parameters, keep_all_below_boundary and
    enforce_left_cutoff

  • Added demonstrations of new models and parameters to vignette

             Changes in version 1.1.3 (2021-08-22)                  
  • Changes made in the vignette

               Changes in version 1.1.2 (2021-08-22)                  
    
  • Link example data on zenodo in vignette

               Changes in version 1.1.1 (2021-06-03)                  
    
  • Addition to miRanda Files

                    Changes in version 1.2.0                        

IMPORTANT: R2 is now reported in percentages for intra, multi and
gain.
Collecting results from running mistyR < 1.1.11 will lead to
miscalcuation of gain.R2. Update the performance.txt files by
multiplying the values in columns intra.R2 and multi.R2 by 100.

                    Changes in version 1.0.3                        
                   Changes in version 6.18.0                        

new features / enhancements / changes

  • new function plotMarkers to visualise the selected features in
    block
    analyses (see #134)
  • auroc title now fixed (#135)
  • cimDiablo takes trim argument to customise outlier filtering (#136)
  • plotIndiv.pca default shape set to 16
  • circosPlot & network now support blocks with similar feature names
  • circosPlot now has methods for block.spls objects
  • circosPlot now takes new formal and advanced args for
    customisation.
    See ?circosPlot.

bug fixes

  • plotVar legend colour mismatch bug fixed
  • plotDiablo error undefined variable (Y) fixed
  • nipals initialisation bug with high-variance high-NA rate column
    fixed
  • cim bug with high NA rate data fixed using imputation by the column
    mean
                   Changes in version 0.99.5                        
  • Updated R/monaLisa-package.R file

                     Changes in version 0.99.4                        
    
  • Suppressed warnings from matchPWM (due to presence of Ns) in
    regression vignette

                     Changes in version 0.99.3                        
    
  • Updated README.md file

                     Changes in version 0.99.2                        
    
  • Added fixes to the regression vignette
  • Addressed failing test in calcBinnedKmerEnr

                     Changes in version 0.99.1                        
    
  • Added examples where missing for exported functions
  • Harmonized function naming (anno_seqlogo -> annoSeqlogo,
    sample_random_regions -> sampleRandomRegions)
  • Clarified details on Pearson residual calculation
  • Adapted documentation for new version of BiocParallel
  • Harmonized return values from plot functions
  • Added legend position and size arguments to plotSelectionProb()

                     Changes in version 0.99.0                        
    
  • Preparation for Bioconductor submission

                      Changes in version 0.2.0                        
    
  • Added a NEWS.md file to track changes to the package.
                    Changes in version 1.0.0                        

Major changes

  • First public version of mosbi. Future changes will be reported
    here.
                   Changes in version 1.37.5                        
  • Change the style of motifPile.

  • Fix the bug of the ylab grid.

                     Changes in version 1.37.4                        
    
  • Fix the bug that the rownames were not checked for alignment.

                     Changes in version 1.37.3                        
    
  • Fix the bug method argument of matAlign is ignored.

                     Changes in version 1.37.2                        
    
  • Improve importMatrix to read the tags from file.

                     Changes in version 1.37.1                        
    
  • handle the error “failed to load cairo DLL”

                    Changes in version 1.1.8                        
  • Fixed test that was resulting in error duet to version 1.1.6
    updated
    way to read the files.

                      Changes in version 1.1.7                        
    
  • Removed parentheses from the news that was causing issues in
    Bioconductor.

                      Changes in version 1.1.6                        
    
  • Bug fixed: If a table was missing, the report was not generated.

                      Changes in version 1.1.5                        
    
  • The plot generated by PlotPTM() will now indicate (in the legend
    title) whether the Post-Translational modifications have been
    aggregated or not as a result of the parameter aggregate_PTMs.

  • The function PlotPeptidesIdentified() and PlotProteinsIdentified()
    now return a plot containing Missing Values, Frequency of Identified
    by Match Between Runs and Frequency of identified by MS/MS. With
    this, the funciton PlotIdentificationType() becomes obsolete.

  • The function PlotProteinCoverage() now can take as input multiple
    UniprotID in a vector format.

  • The function PlotPTMAcrossSamples() now can take as input multiple
    PTM_of_Interest in a vector format.

  • Change in the function make_MQCombined() to read faster the tables
    and reducing the overall time required to generate a report.

                      Changes in version 1.1.4                        
    
  • The function PlotProteinCoverage() now reports the coverage
    individually in each plot rather than the total protein coverage.

  • MQmetrics now is adapted to MaxQuant v.2.x, since the column names
    are different than in MaxQuant v.1.x. MQmetrics will detect the
    MaxQuant version used and read the columns accordingly.

  • Enhanced error message in PlotiRT() and PlotiRTScore() when irt
    peptides are note found. Enhanced error message for
    PlotProteinCoverage() when the UniprotID is not found.

                      Changes in version 1.1.3                        
    
  • Added new function PlotPTMAcrossSamples(), it takes as input one
    PTM
    of interest and shows its intensities across the samples. This
    function is similar to PlotPTM() but in more detail.
  • In the function PlotPTM() a parameter combine_same_residue_ptms has
    been added. It combines multiple PTMs happening in the same residue
    such as: Dimethyl (KR), Trimethyl (KR).

                      Changes in version 1.1.2                        
    
  • Fixed units of time MaxQuantAnalysisInfo() when experiment lasting
    longer than a day.
  • Added new line to MaxQuantAnalyssInfo() showing when the experiment
    ended.
  • Improved aesthethics in the plots from PlotCombinedDynamicRange()
    and PlotAllDynamicRange().

                      Changes in version 1.1.1                        
    
  • Added pagination to PlotiRT() and PlotiRTScore().
  • Updated vignette style to Bioconductor’s.
  • Improved aesthethics of PlotProteinOverlap() and PlotPCA().
                   Changes in version 1.25.3                        
  • further changes to get rid of compiler warnings

                     Changes in version 1.25.2                        
    
  • removed build/ directory from repo to avoid installation problems

                     Changes in version 1.25.1                        
    
  • update of gc

  • minor changes to get rid of compiler warnings

                     Changes in version 1.25.0                        
    
  • new branch for Bioconductor 3.14 devel

                     Changes in version 1.1                         

Changes in 1.1.4

  • Fix wrong database column name for collision energy.

Changes in 1.1.3

  • Change SQL queries to increase performance.

Changes in 1.1.2

  • Fix bug in show,MsBackendMassbankSql.

Changes in 1.1.1

  • Cache precursor m/z to allow faster queries for spectral matching.
                     Changes in version 1.1                         

Changes in 1.1.3

  • Fix issue with MGF files lacking peak data.

Changes in 1.1.2

  • Export precursor charge in the expected format (issue #16).

Changes in 1.1.1

  • Add an example to the vignette describing how to export only
    selected spectra variables to the MGF file.
                    Changes in version 1.0.0                        
  • First bioconductor release of the MsBackendRawFileReader
    package.
                    Changes in version 1.3.0                        
  • Users can now specify the rank of the model to fit by msImpute

  • Added mspip for identification transfer between runs using
    Maxquant results (Beta phase only)

  • Added evidenceToMatrix which creates limma compatible objects
    from MaxQuant evidence table

                    Changes in version 2.19                         

Changes in 2.19.2

  • Fix plot with type = “XIC” to create an empty plot for samples
    without data points (issue #549).

Changes in 2.19.1

  • Add compareChromatograms method.
                   Changes in version 1.19.2                        
                    Changes in version 1.1.1                        
  • Fix filtering steps in vignette: now using
    QFeatures::filterFeatures()
                    Changes in version 1.2.1                        
  • Fixed a bug related to SRM inputs.
             Changes in version 2.2.3 (2021-10-06)                  
  • Minor change: fix the bug when df.prior is infinite

               Changes in version 2.2.2 (2021-09-21)                  
    
  • Major change: extend groupComparisonTMT() function to cover
    repeated measures design

  • Allow flexible order of condition in dataProcessPlotsTMT.

  • Fix bug in Condition label in dataProcessPlotsTMT.

  • Improve MSstatsTestSingleProteinTMT() by directly reading
    lmerTest output. This may make statistics slightly different
    due to different numeric accuracy

  • fix bug when condition name contains ‘group’

  • change the x-axis order in profile plot

               Changes in version 2.0.1 (2021-06-14)                  
    
  • update comments of PD converter function

  • fix bug in proteinSummarization() function when MBimpute = F

                   Changes in version 1.20.0                        

Bug fixes and minor improvements

  • Avoid dropping experiments with repeated calls to subsetByColData
    and remove harmonization (@cvanderaa, #302)
  • getWithColData suppresses messages from natural subsetting
    operations by default with verbose = FALSE (@bhagwataditya, #301)
  • getWithColData was using the old default (drop = TRUE) and causing
    an error when the experiment is empty (@danielinteractive, #300).
  • Calls to the internal .harmonize operation are reduced to increase
    memory efficiency, when identical experiment colnames present
    (@LTLA, #299).
  • subsetByColData now errors on subscript vectors longer than the
    nrow
    of the colData (previously a warning).
  • colData<- includes a check for identical row names. If so, direct
    replacement of the colData occurs without harmonization.
  • Added a warning when an empty sampleMap is provided in the
    constructor function which may cause unexpected behavior.
    Documentation is updated to include more details on the sampleMap
    input.
             Changes in version 2.0.0 (2020-11-23)                  
  • Update selection of significant results in the ‘topDirs’ function.
    Major change,
    results will be more strict compared to pre-2.0.0 version

  • Removed ‘BLMA’ and ‘metap’ dependency, added ‘aggregation’ dependency

  • P-values are aggregated using ‘max’ by default. I.e., for a region
    differentially
    interacting with multiple regions, a maximum p-value will be
    selected. Fisher,
    Lancaster, and Sidak methods are also available

  • Harmonize counting of significant regions using ‘p.adj_cutoff’ only
    (‘alpha’
    cutoff removed)

  • The ‘manhattan’ function is harmonized with ‘topDirs’

  • The ‘perm_test’ function is harmonized with ‘topDirs’

  • Update vignettes to match functions

                   Changes in version 1.1.27                        

Bug fixes

  • validate_parameters can now handle ref_genome=NULL
  • .tsv.gz no longer assigned suffix .tsv.
  • Made code width <80 characters.
  • Changed to_GRanges/to_GRanges functions to all-lowercase functions
    (for consistency with other functions).
  • Set nThread=1 in data.table test functions.

New Features

New Features

  • Extra mappings for FRQ column, see data(“sumstatsColHeaders”) for
    details

                     Changes in version 1.1.23                        
    

New Features

  • format_sumstats(FRQ_filter) added so SNPs can now be filtered by
    allele frequency
  • Mapping file now has mappings for allele frequency (AF) to FRQ
  • VCF files with AF in INFO column e.g. ‘AF=…’ now converted to AF
    column
  • format_sumstats(frq_is_maf) check added to infer if FRQ column
    values are minor/effect allele frequencies or not. frq_is_maf allows
    users to rename the FRQ column as MAJOR_ALLELE_FRQ if some values
    appear to be major allele frequencies

                     Changes in version 1.1.19                        
    

New Features

  • get_genome_builds() can now be called to quickly get the genome
    build without running the whole reformatting.
  • format_sumstats(compute_n) now has more methods to compute the
    effective sample size with “ldsc”, “sum”, “giant” or “metal”.
  • format_sumstats(convert_ref_genome) now implemented which can
    perform liftover to GRCh38 from GRCh37 and vice-versa enabling
    better cohesion between different study’s summary statistics.

                     Changes in version 1.1.11                        
    

Bug fixes

  • check_no_rs_snp can now handle extra information after an RS ID. So
    if you have rs1234:A:G that will be separated into two columns.
  • check_two_step_col and check_four_step_col, the two checks for when
    multiple columns are in one, have been updated so if not all SNPs
    have multiple columns or some have more than the expected number,
    this can now be handled.
  • Extra mappings for the FRQ column have been added to the mapping
    file

New Features

New Features

  • import_sumstats reads GWAS sum stats directly from Open GWAS. Now
    parallelised and reports how long each dataset took to import/format
    in total.
  • find_sumstats searches Open GWAS for datasets.
  • compute_z computes Z-score from P.
  • compute_n computes N for all SNPs from user defined smaple size.
  • format_sumstats(ldsc_format=TRUE) ensures sum stats can be fed
    directly into LDSC without any additional munging.
  • read_sumstats, write_sumstas, and download_vcf functions now
    exported.
  • format_sumstats(sort_coordinates=TRUE) sorts results by their
    genomic coordinates.
  • format_sumstats(return_data=TRUE) returns data directly to user.
    Can
    be returned in either data.table (default), GRanges or VRanges
    format using format_sumstats(return_format=”granges”).
  • format_sumstats(N_dropNA=TRUE) (default) drops rows where N is
    missing.
  • format_sumstats(snp_ids_are_rs_ids=TRUE) (default) Should the SNP
    IDs inputted be inferred as RS IDs or some arbitrary ID.
  • format_sumstats(write_vcf=TRUE) writes a tabix-indexed VCF file
    instead of tabular format.
  • format_sumstats(save_path=…) lets users decide where their
    results
    are saved and what they’re named.
  • When the save_path indicates it’s in tempdir(), message warns users
    that these files will be deleted when R session ends.
  • Summary of data is given at the beginning and the end of
    format_sumstats via report_summary().
  • Readability of preview_sumstats() messages improved.
  • New checks standard error (SE) must >0 and BETA (and other effect
    columns) must not equal 0:
    format_sumstats(pos_se=TRUE,effect_columns_nonzero=TRUE)
  • Log directory containing all removed SNPs is now available and can
    be changed to a different directory by setting:
    format_sumstats(log_folder_ind=TRUE,log_folder=tempdir())
  • All imputed data can now be identified with a column in the output
    using: format_sumstats(imputation_ind=TRUE)
  • Users can now input their own mapping file to be used for the
    column
    header mapping in place of data(sumstatsColHeaders). See
    format_sumstats(mapping_file = mapping_file).

Bug fixes

Bug fixes

  • Preprint publication citation added.
                    Changes in version 1.7.2                        
  • bug fix in prepSim(): removal of NA coefficients and
    subsetting of the input SCE was previously out of synch
             Changes in version 1.3.1 (2021-10-10)                  
                   Changes in version 2.27.1                        
                    Changes in version 2.0.0                        
  • Major changes to plot_agg_regions().
  • Features of plot_agg_regions() and
    plot_agg_regions_sample_grouped() merged into one interface.
  • Regions now specified using single table.
  • Changed plot_regions() default window proportion to 0.
  • Changed default theme from theme_bw() to theme_tufte().
  • Added Megalodon data import instructions to “Importing Data”
    vignette.
  • Added scico palette defaults for heatmaps. These are colourblind
    friendly.
  • Added check for 0 length queries which would cause program to hang
    indefinitely.
  • Added setters for NanoMethResult attributes methy, samples and
    exons.
  • Added MDS and PCA plots.
  • Added vignette for using external annotation and dimensionality
    reduction.
  • Added binary thresholding for plot_gene(), plot_region() and
    plot_agg_regions().
  • Added regions argument to bsseq_to_edger() to calculate aggregate
    counts over features rather than per site.
             Changes in version 1.1.2 (2020-09-28)                  
  • Update license

               Changes in version 1.1.1 (2020-08-13)                  
    
  • Documentation updates

  • Handle new parameters from ggiraph update

               Changes in version 1.1.0 (2020-05-19)                  
    
  • Initial Bioconductor devel 3.14 version

                   Changes in version 0.99.0                        
                    Changes in version 1.3.3                        

Changes

Changes

  • include ability to iteratively acquire and visualize Bkg std error

  • new arguments to choose whether to calculate Bkg std error

  • accomodate StereoGene version 2.22, esp. seeding of analysis

  • better run analysis on track files outside local directory

                    Changes in version 1.5.3                        
  • Moved RCy3, scater, clusterExperiment and netSmooth to “Suggests” to
    reduce dependency burden

  • Sped up vignettes by limiting all to binary classification and
    limiting number of layers

  • Removed TL;DR from vignettes as usefulness in question but
    maintainance high.
    Developers notes:

  • Added Dockerfile and Github Actions for automated testing

  • GHA auto-generates a Docker image with netDx which gets pushed to
    shraddhapai/netdx_devenv

                      Changes in version 1.5.2                        
    
  • Added wrapper functions for ease-of-use. Includes:

  • getResults() to plot results of running the predictor

  • getPSN() for creating and visualizing integrated PSN

  • confusionMatrix() to visualize confusion matrix

  • tSNEPlotter() to visualize tSNE of integrated PSN (doesn’t require
    Cytoscape)

  • Added CITATION file with citations to netDx methods and software
    paper

                      Changes in version 1.5.1                        
    
  • Adding support for Java 16.

  • Disabling CNV-based vignette to allow other three vignettes to run
    without causing build timeout on devel system

             Changes in version 1.53.2 (2021-07-28)                 
  • rmarkdown added as a dependency to fix Bioc build
                    Changes in version 1.9.3                        
                   Changes in version 1.18.2                        
  • Changed deprecated ‘GenomeInfoDb::fetchExtendedChromInfoFromUCSC’ to
    ‘GenomeInfoDb::getChromInfoFromUCSC’ in R/methods.R

                     Changes in version 1.18.1                        
    
  • Fixing R 4.1.0 _R_CHECK_LENGTH_1_LOGIC2 error in
    tests/testthat/utils.R:applyMap
    by using inherits() instead of class() to account for hadleyverse

                    Changes in version 1.0.0                        
  • nullranges is released on Bioconductor! the package offers the
    creation of null genomic feature sets, either through sampling from
    a pool in order to match covariates with a particular focal set, or
    via block bootstrapping of features optionally with respect to a
    genome segmentation. Critically, nullranges is designed as a modular
    package, solely for the purpose of generating null feature sets, and
    to be used in conjunction with another package for calculating
    overlaps, such as GenomicRanges or plyranges. Let us know your
    comments, suggestions or feedback on Bioconductor support site or
    through GitHub Issues.
            Changes in version 0.99.12 (2021-10-26)                 
  • Fixed bug in MakeSE() and CoordToGR()

              Changes in version 0.99.10 (2021-10-20)                 
    
  • Accounts for when NxtIRFdata cannot fetch data from ExperimentHub

               Changes in version 0.99.9 (2021-10-20)                 
    
  • Added GetCoverageBins()

  • Add warning in IRFinder if coordinate sorted BAM file takes too long
    to run.

  • Fixed missing coverage data at both ends of plot track.

               Changes in version 0.99.8 (2021-10-13)                 
    
  • Fixed memory leak when writing COV files

               Changes in version 0.99.6 (2021-10-12)                 
    
  • Added GetCoverageRegions() which calculates the mean coverage of each
    region
    in a given GRanges object

  • Added BAM2COV() which calculates and creates COV files from BAM files

               Changes in version 0.99.2 (2021-10-07)                 
    
  • Fixed bug in Find_FASTQ

               Changes in version 0.99.0 (2021-09-29)                 
    
  • Bioconductor Release

                   Changes in version 0.99.0                        

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.
                    Changes in version 3.2.0                        
  • New resource: PrePPI
  • Configuration option to completely disable logging to file
  • New vignettes: Path reconstruction, and Bioconductor 2021 Workshop
  • Many minor bugfixes and improvements
             Changes in version 3.1.2 (2021-10-06)                  
  • Better test of poset transformation

               Changes in version 3.1.1 (2021-10-06)                  
    
  • XOR, AND, OR dependencies: plots of DAGs honor all possible values.

  • Few miscell minor changes.

                    Changes in version 3.11                         

Enhancements

  • Allow control of mininum number of events for each step of
    GatingTemplate #298

Bug Fixes

API Changes

Simple renaming

Bug Fixes

  • Some minor fixes to gt_toggle_helpergates
  • Fix “positive” argument to gate_mindensity to match doc
                   Changes in version 2.11.1                        
  • multiple bugfixes e.g. caused by tsne package
                   Changes in version 1.13.7                        

SIGNIFICANT USER-VISIBLE CHANGES

  • Massive improvement in speed of coveragePerTiling

  • Improved p-shifting analysis (also added verbose output)

  • Added possible optimization for annotation

  • Rewritten vignettes

                   Changes in version 0.99.9                        

New Features

  • Replaced R-CMD GHA with bioc-check GHA.
  • Added new badges.

Fixes

New Features

New Features

  • Added new function create_background.
  • Added new function infer_species.
  • report_orthologs and convert_orthologs can now handle cases where
    input_species is the same as output_species.
  • Add internal function get_all_orgs to easily list all organisms
    from
    different packages.
  • Added all_genes method “babelgene”.

Fixes

Fixes

New Features

Fixes

New Features

  • orthogene released to Bioconductor.
              Changes in version 1.3 (2021-10-14)                   
  • Minor bug change for lists of data.frame vs matrix for ExperimentList
             Changes in version 0.99.0 (2021-09-21)                 
  • Submitted to Bioconductor
                   Changes in version 2.20.0                        

Other notes

  • the tables in the PCA2GO tab panel can be compacted only if they
    are
    computed via the pca2go function (offline) – at runtime,
    limmaquickpca2go is used and no compaction is required
  • if an annotation is provided with a column gene_id, these values
    are
    actually overwriting the rownames (makes the object more robust with
    respect to its provenance)
                    Changes in version 2.6.0                        
  • added max.overlaps and min.segment.length to provide further control
    over
    connectors. max.overlaps replaces maxoverlapsConnectors, but both can
    still
    be used for legacy purposes
             Changes in version 1.7.1 (2021-06-21)                  
                    Changes in version 0.1.0                        
                    Changes in version 2.5.3                        
  • Added PharmacoSet2 constructor to allow creation of PSets with
    updated class definition introducted in BioC 3.13
  • The sensitivity slot is now required to be a
    TreatmentResponseExperiment
  • The molecularProfiles slot is now required to be a
    MultiAssayExperiment
  • The original constructor and all accessors remain in the package
    for
    full backwards compatibility

                      Changes in version 2.5.2                        
    
  • Fix: remove ‘fdr’ item from geneDrugSensitivity return vector

                      Changes in version 2.5.1                        
    
  • Fix: reverted GDSCsmall.rda and CCLEsmall.rda to original data
    format; they were accidentally pushed with MultiAssayExperiments in
    @molecularProfiles

                      Changes in version 2.5.0                        
    
  • Spring Bioconductor release!
                   Changes in version 1.19.1                        

USER-VISIBLE CHANGES

  • Added support for TreeSummarizedExperiment class

  • Added support for phyloseq class

  • Updated vignette

  • Changed main argument name from df to x

INTERNAL

  • Implemented philr as S3 method
             Changes in version 1.1.1 (2021-08-05)                  
  • Added propReads() function to calculate the proportion of sample
    reads pulled by each peptide.
  • Added coercion function to convert a PhIPData object to a DataFrame
    (and consequently also data.frames and tibbles).
  • Changed the storage of alias, library, and beads-only indicators to
    package environment variables rather than global variables.
                    Changes in version 1.2.1                        
  • Included Cell Reporta citation
  • rainbow colour palette is used for plotQC function
                    Changes in version 1.7.8                        
  • only mainInput is required in config file

                      Changes in version 1.7.7                        
    
  • use config file for input files, refspec selection and othes
    settings

                      Changes in version 1.6.6                        
    
  • turn off auto sizing for large number of taxa or genes (>=
    10.000)

                      Changes in version 1.6.5                        
    
  • fixed filter for “species relation”

  • added midpoint colors

                      Changes in version 1.6.2                        
    
  • increase default font size for profile and domain plot

  • make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam,
    smart

                      Changes in version 1.6.1                        
    
  • modified taxonomy ranks (ropensci#875)

  • improved rank indexing function (ropensci#874)

  • improved x-axis label (#116)

            Changes in version 1.19.50 (2021-10-14)                 

New functions

  • Neda added the identify.modules(), make.filter(), and
    apply.filter() functions, but not exported them yet.

              Changes in version 1.19.30 (2021-09-08)                 
    

Bug Fixes

  • The averaged.network() function does not have the nodes
    argument in bnlearn Version >=4.7, and thus this argument was
    removed.

              Changes in version 1.19.24 (2021-08-06)                 
    

New functions

  • The get.enriched.pw() function is added.

Bug Fixes

Changes in existing functions

Bug Fixes

  • The C50 plot function seems to have different behavior when the
    number of Labels is 2. Habil reverse the color to fix the
    resulting bug.
                   Changes in version 1.65.1                        
  • new feature:
    –allow parameter Prefix' in run.plgem’ to be passed down to
    plgem.fit' when writeFiles=TRUE’

  • bug fix:
    –only check existence of fittingEvalFileName' when both
    fittingEval’ and
    plot.file' are TRUE in plgem.fit’

  • new feature:
    –added parameter Prefix' to run.plgem’ to be passed down to
    plgem.write.summary' when writeFiles=TRUE’

  • bug fix:
    –fixed error occurring when running run.plgem' with plotFile=TRUE’

                   Changes in version 0.99.11                       

BUG FIXES

o : added back to readHic for strawr region parsing.
o plotHicSquare subsetting fixed for off diagonal regions.

NEW FEATURES

o All Hi-C functions now allow input of remote Hi-C files.

                   Changes in version 0.99.9                        

This package was previously called BentoBox.

                   Changes in version 0.99.0                        

NEW FEATURES

o Version bump to 0.99.0 for Bioconductor package submission.
o bb_mapColors function for users to map a vector to a palette
of colors.
o linecolor parameter in bb_plotPairs, bb_plotPairsArches,
and bb_plotRanges now accepts a single value, a vector of colors,
a colorby object, or the value “fill”.

                  Changes in version 0.0.0.14                       

BUG
FIXES

o R version requirement changed to (R >= 4.1.0) for proper plot
placement.

NEW
FEATURES

o colorby object now has a scalePerRegion parameter to scale
numerical
colorby data to the range of data in a plotted genomic region.

                  Changes in version 0.0.0.13                       

SIGNIFICANT USER-VISIBLE CHANGES

o bb_plotManhattan fill paramete now accepts a single value,
a vector of colors, or a colorby object.

                  Changes in version 0.0.0.12                       

SIGNIFICANT USER-VISIBLE CHANGES

o colorby constructor now includes optional palette specification.
o bb_plotPairs, bb_plotPairsArches, and bb_plotRanges fill
parameter
now accepts a single value, a vector of colors, or a colorby
object.

BUG FIXES

o GInteractions assembly match checking moved before dataframe
conversion.

                  Changes in version 0.0.0.11                       

SIGNIFICANT USER-VISIBLE CHANGES

o Data moved to plotgardenerData package.
o Default genome assembly updated to “hg38”.

BUG FIXES

o Streamlined parameter parsing and data reading logic.

                  Changes in version 0.0.0.10                       

NEW FEATURES

o Added unit tests with testthat.
o bb_annoDomains function addition.
o bb_plotSignal vertical orientation.

                   Changes in version 0.0.0.9                       

NEW FEATURES

o Added a NEWS file to track changes to the package.

BUG FIXES

o Updated viewport parsing for package grid version 4.1.0.

             Changes in version 1.1.1 (2021-06-09)                  
  • Implemented use of Reference well for control channel
                   Changes in version 1.25.1                        
  • adjusted NAMESPACE to account for changes in BiocGenerics package

                     Changes in version 1.25.0                        
    
  • new branch for Bioconductor 3.14 devel

                   Changes in version 1.99.3                        
  • NB function now exported

  • note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

                     Changes in version 1.99.2                        
    
  • bug fix in fragment generation (last 2 bases of transcript were never
    sequenced)

             Changes in version 1.3.3 (2021-09-28)                  
  • The default for MinPts DBSCAN parameter has been changed to 100

               Changes in version 1.3.2 (2021-09-21)                  
    
  • Vignette edits

               Changes in version 1.3.1 (2021-07-19)                  
    
  • Change y of x.y.z version number to comply with the release

  • Add MD as a maintainer

                    Changes in version 1.3.3                        
                   Changes in version 2.21.1                        
           Changes in version 2020-10-14 (2020-10-14)               
  • Model matrices are not accessed in the local and not in the global
    enviroment

             Changes in version 2020-09-01 (2020-09-01)               
    
  • Fixed issue with rownames when using Progeny with Permutations
    function

             Changes in version 2020-06-09 (2020-06-09)               
    
  • Website: Google Analytics

             Changes in version 2020-04-27 (2020-04-27)               
    
  • PROGENy website development

Major update with the following main points:

  • Added the mouse model matrix containing 14 pathways

  • The human model matrix extended to 14 pathways

  • Added the following functions: progenyPerm, progenyScatter,
    progenySavePlots, getModel

  • Added tests and test data

  • Added the vignette for usage the PROGENy on single-cell RNA-seq
    data

  • Added functionality to work with Seurat objects

                    Changes in version 1.33                         
                     Changes in version 1.0                         
  • Initial release of ProteoDisco (v1.0.0).
                   Changes in version 1.25.1                        
  • add bin, compareChromatograms and compareSpectra

                     Changes in version 1.25.0                        
    
  • Bioc devel (3.14) version bump

                   Changes in version 1.20.0                        

ShinyProxy support

  • psichomics(): add argument shinyproxy; when set to TRUE, change set
    of options to viably run in ShinyProxy
  • Avoid automatically closing the app
  • Replace custom file browsers with shiny’s versions
  • Fix issues with progress bar
  • Include ShinyBS JavaScript library
  • Upload files using default file browser input and allow to upload a
    ZIP folder instead of a folder

Bug fixes

  • Fix issues with Shiny 1.7.0:
  • Change icon names as required by newest versions of font-awesome
  • Avoid modifying Shiny tags using generic positions
  • Load recount data (visual interface):
  • Improve responsiveness of project selection
  • Splicing annotation (visual interface):
  • Load annotation only when opening the splicing quantification
    tab
  • Automatically select hg38 if using GTEx v8 data
  • PCA plot (visual interface):
  • Automatically plot PCA after calculating PCA scores
  • Copy-edit text
  • Fix specific errors related with PCA analysis of only one group
  • Diagrams of alternative splicing events:
  • Fix wrong coloring of reference exon used for AFE and A5SS
    events
  • Transcript plot:
  • Orange region (the reference exon) is now on top of blue region

                     Changes in version 1.18.5                        
    
  • Diagrams of alternative splicing events:
  • Fix wrong coloring of reference exon used for AFE and A5SS
    events
  • Transcript plot:
  • Avoid alternative regions from overlapping
  • Fix loading twice when selecting a new event (visual interface)

                     Changes in version 1.18.4                        
    
  • psichomics(): fix visual interface not launching
  • getGtexReleases() not properly retrieving whether future GTEx
    releases (9 and higher) are available
  • Remove warning related with TCGA data when MD5 checks fail

                     Changes in version 1.18.3                        
    
  • plotSplicingEvent(): avoid opening browser window in
    non-interactive
    contexts
  • Fix Bioconductor build report’s timeout when creating vignettes on
    Windows

                     Changes in version 1.18.2                        
    
  • Fix issues with unit tests in Bioconductor

                     Changes in version 1.18.1                        
    
  • Fix issues with unit tests in Bioconductor
  • Improve Docker images:
  • Simplify Dockerfile
  • Store Docker images in GitHub Container Registry
  • Automatically build latest Docker image based on last release
    version
  • Improve README with install instructions for GitHub and Docker
  • Minor copy-editing of user-provided data tutorial
  • Fix minor spelling issues
             Changes in version 1.1.4 (2021-09-23)                  
  • removal of the loaded prtset data to avoid any local path problems

               Changes in version 1.1.1 (2021-09-13)                  
    
  • Added graphical interface

                    Changes in version 2.0.0                        

NEW FEATURES

  • Report median absolute pairwise difference (MAPD) of tumor vs normal
    log2
    ratios in runAbsoluteCN

  • Improved mapping bias estimates: variants with insufficient
    information
    for position-specific fits (default 3-6 heterozygous variants)
    are clustered and assigned to the most similar fit

  • Make Cosmic.CNT INFO field name customizable

SIGNIFICANT USER-VISIBLE CHANGES

  • Cleanup of naming of command line arguments (will throw lots of
    deprecated
    warnings, but was long overdue)

  • More robust alignment of on- and off-target tumor vs normal log2
    ratios.
    Ratios are shifted so that median difference of neighboring
    on/off-target
    pairs is 0. This should fix spurious segments consisting of only on-
    or
    off-target regions in high quality samples where those minor off-sets
    sometimes exceeded the noise.

  • Added min.variants argument to runAbsoluteCN

  • Added PureCN version to runAbsoluteCN results object (ret$version)

  • Addressed observed over-segmentations in very clean data:
    • Do not attempt two-step segmentation in PSCBS when off-target noise
      is
      still very small (< 0.15, min.logr.sdev in runAbsoluteCN)
    • Increase automatically determined undo.SD in all segmentation
      functions
      when noise is very small (< min.logr.sdev)
    • min.logr.sdev is now accessible in PureCN.R via –min-logr-sdev
  • Added pairwise sample distances to normalDB output object helpful for
    finding noisy samples or batches in normal databases

  • Do not error out readCurationFile when CSV is missing and directory
    is not writable when re-generating it (#196)

  • Add segmentation parameters as attributes to segmentation data.frame

  • Added min.betafit.rho and max.betafit.rho to calculateMappingBias*

  • Made –normal_panel in PureCN.R defunct

  • Added GATK/Picard header with sequence lengths to interval file,
    added readIntervalFile function to parse it

BUGFIXES

  • Fix for crash when –normal_panel in NormalDB.R contained no variants
    (#180).

  • Fix for crash when rtracklayer failed to parse –infile in
    FilterCallableLoci.R (#182)

  • More robust parsing of VCF with missing GT field (#184)

  • Fix for bug and crash when mapping bias RDS file contains variants
    with
    multiple alt alleles (#184)

  • Added missing dependency ‘markdown’

  • Fix for crash when only a small number of off-target intervals pass
    filters (#190)

  • Fix for crash when PSCBS segmentation was selected without VCF file
    (#190)

  • Fix for crash when Hclust segmentation was selected without
    segmentation
    file (#190)

  • Fix for crashes when not many variant pass filters (#192, #195)

  • Fix for crash when provided segmentation does not have chromosomes
    in common with VCF (#192) or does not provide all chromosomes present
    in
    the coverage file (#192)

                    Changes in version 1.31                         

qcmetrics 1.31.1

  • Suggest rmarkdown to fix build error
             Changes in version 1.29.6 (2021-10-23)                 

BUG FIXES

  • segmentBins() would report the sample names as “NA” in output
    messages
    if the sample name contained hyphens, or other symbols automatically
    replaced by data.frame(…, check.names = TRUE). This was a harmless
    bug.

               Changes in version 1.29.5 (2021-10-20)                 
    

PERFORMANCE

  • All internal row and column-based matrixStats calls now avoids
    overhead
    from handling row and column names.

MISCELLANEOUS

DOCUMENTATION

  • Vignette now illustrate parallelization using the ‘multisession’
    future
    strategy, instead of the deprecated ‘multiprocess’ strategy.

DEPRECATION AND DEFUNCT

  • Argument ‘seeds’ of segmentBins() is defunct. It has been deprecated
    and
    ignored since QDNAseq 1.21.3 (September 2019).

               Changes in version 1.29.3 (2021-10-04)                 
    

NEW FEATURES

SOFTWARE QUALITY

BUG FIXES

  • exportBins(fit, format = “seg”, …) and format = “vcf” would merge
    segments with equal copy-number calls if they were interweaved with
    copy-neutral segments.

  • exportBins(fit, format = “seg”, …) and format = “vcf” produced an
    obscure
    error with messages “Error in dimnames(x) <- dn : length of
    ‘dimnames’ 2
    not equal to array extent” for samples with no copy-number
    abberations.

  • exportBins(fit, format = “seg”, file = …) and format = “vcf” did
    not
    respect argument ‘file’ but instead wrote files of its own names to
    the
    current working directory.

  • exportBins() would corrupt option ‘scipen’. Now it is left
    unchanged.

KNOWN ISSUES

  • callBins() produces warnings on “Recycling array of length 1 in
    vector-
    array arithmetic is deprecated. Use c() or as.vector() instead.” in
    R (>= 3.4.0). This is a problem in the package ‘CGHcall’ dependency
    and
    is something that needs to be fixed there. For further details,
    please
    see github.com/tgac-vumc/CGHcall/issues/2.

               Changes in version 1.29.2 (2021-09-22)                 
    

SOFTWARE QUALITY

BUG FIXES

  • binReadCounts() would fail when specifying argument ‘chunkSize’. The
    fix
    was to require ‘future’ package version 1.22.1 or newer.

               Changes in version 1.29.1 (2021-08-26)                 
    

SOFTWARE QUALITY

  • Add package test for binReadCounts().
                    Changes in version 1.3.0                        

QFeatures 1.3.6

  • New feat3 example data to demonstrate and test more complex
    AssayLinks structure.
  • Improved the plot,QFeautres function to avoid cluttering of nodes.
  • Adapted the visualization vignette using feat3.

QFeatures 1.3.5

  • Add plot,QFeatures and visualisation vignette.

QFeatures 1.3.4

  • Fixed bug that produced invalid AssayLinks when using filterNA.

QFeatures 1.3.3

  • Improved validity checks on AssayLinks
  • Fixed the subsetting of AssayLinks to ensure consistent data

QFeatures 1.3.2

  • Add logo to package
  • Fix class coercion error (see #b9ce7f1e9)

QFeatures 1.3.1

  • Added rbindRowData: a function to select variables in the rowData
    and bind it in a single DataFrame
  • Added rowData<-: this new method replaces replaceRowDataCols to
    offer a more standardize functionality.
  • Added a new section in the QFeatures vignette to expand on how to
    manipulate the metadata within a QFeatures object

QFeatures 1.3.0

  • New devel version (Bioc 3.14)
             Changes in version 1.9.2 (2021-09-01)                  
                   Changes in version 1.34.0                        

USER-VISIBLE CHANGES

                   Changes in version 1.18.0                        

New features

  • Sparse matrices of dgCMatrix type can now be coerced to
    RaggedExperiment when rownames are coercible to GRanges

Bug fixes and minor improvements

  • ‘counts’ set as the default name for the values in mcols after
    coercion from dgCMatrix
             Changes in version 1.1.2 (2021-05-28)                  
  • reviewers’ suggestions were implemented, docs updated, typos fixed

  • new methods for simulation of AMR and test data sets

  • NULL as a default for data.samples (to use all)

  • doRNG is used to ensure reproducibility during parallel computing

  • a couple of new defaults for previously required parameters for easy
    usage

               Changes in version 1.1.0 (2021-05-21)                  
    
  • released at bioconductor

              Changes in version 1.1 (2021-05-31)                   
  • Improved error handling of system2 call in .rawrrSystem2Source
    by logging stdout and stderr and make them available from the R
    console.

  • Added helper function .checkReaderFunctions.

                   Changes in version 2.14.0                        
             Changes in version 1.7.5 (2021-09-28)                  
  • Fixed documentation of “plot_heatmap”

               Changes in version 1.7.4 (2021-09-24)                  
    
  • Added new plotting function “plot_heatmap”

               Changes in version 1.7.3 (2021-09-14)                  
    
  • Updated vignette to introduce the “open_reactome” command

               Changes in version 1.7.2 (2021-09-09)                  
    
  • Fixed timeout issue during large requests in
    perform_reactome_analysis

               Changes in version 1.7.1 (2021-06-09)                  
    
  • Fixed bug in scRNA-seq vignette.

                   Changes in version 1.19.2                        

BUG FIXES

                    Changes in version 1.3.9                        

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

                    Changes in version 1.3.1                        
             Changes in version 1.5.3 (2021-08-04)                  
  • Updated formatting of consensus secondary structure queries to match
    changes made by Rfam
                   Changes in version 1.12.2                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

NEW FEATURES

  • Added new function show_all_metadata()

SIGNIFICANT USER-VISIBLE CHANGES

  • removed is_GMQL from read_gmql function
    The entire dataset must have the right folder structure in order to
    works correctly —>

  • Swap order of arguments ‘dir_out’ and ‘name’ of the collect()
    function so now the latter comes before the former.

DEPRECATED AND DEFUNCT

BUG FIXES

  • fixed the remote processing
                   Changes in version 2.38.0                        

NEW FEATURES

  • Added support for reading attributes where the datatype is
    either a 64-bit or unsigned 32-bit integer.

  • Added many functions for working with file creation property
    lists. (Thanks to @ilia-kats for the contribution,
    github.com/grimbough/rhdf5/pull/95)

  • Added support for variable length and UTF-8 encoded string
    datasets. (Thanks to Aaron Lun @LTLA for the contribution,
    github.com/grimbough/rhdf5/pull/88)

CHANGES

  • Documentation switched to roxygen2

BUG FIXES

  • h5createDataset() now prints a warning if a chunk dimension
    exceeds the maximum size of that dimension and automatically
    sets the corresponding chunk dimension to the maxiumum.
    (Thanks to Eric Kernfeld @ekernf01 for the report,
    github.com/grimbough/rhdf5/issues/97)
                    Changes in version 1.16                         

Bug fixes

  • AR and RANLIB programs used to compile R are now also used to compile
    the HDF5 library. This resolves issue when the default versions found
    on a
    system are incompatible with options used to build R.
    (thanks to @miesav, github.com/grimbough/Rhdf5lib/pull/41)

  • Fixed issue in Windows installation introduced by upstream changes
    to libcurl distributed by rwinlibs.
    (github.com/grimbough/Rhdf5lib/pull/42)

                   Changes in version 0.99.11                       

Package

  • Base class
  • RLRanges stores R-loop data and RLSeq results.
  • Workflow -The wrapper function RLSeq() performs all analysis steps.
    However, individual functions are also accessible.
  • Model
  • The model for predicting sample quality label is updated to the
    latest version, incorporating 231 samples in training. This
    model showed high accuracy (.9304) on a test set of 115 samples.

Status

Pre-release. This version is prior to the first official release
(v1.0.0), anticipated in Oct. 2021.

                   Changes in version 0.99.0                        
  • Submitted to Bioconductor
             Changes in version 1.7.1 (2021-07-27)                  
                    Changes in version 2.21                         

CHANGES IN VERSION 2.21.1

CHANGES IN VERSION 2.21.0

  • New devel version for Bioc 3.14
                   Changes in version 1.99.01                       
  • no bug, but removed extra files from man folder
             Changes in version 1.49.1 (2021-07-28)                 
  • rmarkdown added to dependency to fix bioc builds
                     Changes in version 2.1                         

rpx 2.1.12

  • Annotate additional experiments as returning errors (see issues for
    full list) <2021-10-07 Thu>

rpx 2.1.11

  • Annotate PXD012095 as returning an error (see #12) <2021-10-04 Mon>

rpx 2.1.10

  • Caching PRIDE sitemap with all PXD projects.
  • New pxinstruments(), pxptms() and pxprotocols() accessors.

rpx 2.1.9

  • Internal function to tally local project vs full PX.

rpx 2.1.8

  • New PXDataset2 class with richer interface and more stable data
    downloading functions. PXDataset and PXDataset2 work transparently
    and PXDataset2 is now default.

  • Add deprecation notice in PXDataset() constructor.

rpx 2.1.7

  • Improve object creating printout.
  • Improve pxCachedProjects() output.

rpx 2.1.6

  • Update installation instruction in README.md.
  • Cache location is now also stored inside the PXDataset object.
  • New pxCacheInfo() function and use it to show caching info in
    show,PXDataset.

rpx 2.1.5

rpx 2.1.4

  • Fix bug in PXDdataset internal data storage.

  • New pxCachedProjects() function that return the cached projects.

  • Fixes and improvements in the documentation.

rpx 2.1.3

rpx 2.1.2

  • New feature: PXDataset objects now query and store data (ref, tax,
    files, url) when generated instead of fetching these on the fly
    every time. This new feature has been added to circumvent the issues
    with data access (see #5).

rpx 2.1.1

  • pxannouced() paused (see #7).
                    Changes in version 1.5.4                        
  • scatterPlot() doesn’t warn anymore that we’re using a deprecated
    parm to remove the guide

                      Changes in version 1.5.1                        
    
  • calculateSimMatrix() now allows using arbitrary keys from Orgdb
    packages. Credit: illumination-k. Thanks!

                    Changes in version 2.10                         

DEPRECATED AND DEFUNCT

  • (v 2.9.1) Deprecate applyPileups() in favor of pileup().
                   Changes in version 2.24.0                        

Bug fixes and minor improvements

  • The deprecated functionality vignette moved to the
    vignettes/analysis/ folder
                   Changes in version 1.14.0                        
                   Changes in version 0.32.0                        

SIGNIFICANT USER-VISIBLE CHANGES

  • Subsetting a DataFrame object by row names no longer uses partial
    matching.
            Changes in version 0.99.25 (2021-06-25)                 
  • fixed a recent bug preventing the recognition of many slicing sites
                   Changes in version 1.22.0                        
  • Rename colour_columns_by in plotHeatmap to color_columns_by to
    match other arguments.

  • Add color_rows_by and row_annotation_colors arguments to
    plotHeatmap, similar to analogous column arguments.

  • Change text_by annotations in plotReducedDim to use
    geom_text_repel from ggrepel.

             Changes in version 1.7.3 (2021-07-26)                  
  • scDblFinder now includes both cluster-based and random modes for
    artificial doublet generation

  • thresholding has been streamlined

  • default parameters have been optimized using benchmark datasets

  • added the directDblClassification method

             Changes in version 1.17.1 (2021-07-21)                 
                    Changes in version 1.5.2                        
  • remove loading warnings

                      Changes in version 1.5.1                        
    
  • update vignette

                    Changes in version 1.3.3                        
  • docs: included QFeatures plot in the vignette
  • docs: created a vignette about advanced usage of scp

                      Changes in version 1.3.2                        
    
  • feat: computeSCR now allows for user supplied function that will
    summarize the values from multiple samples and multiple carrier.
  • docs: used more standard variable names in scp vignette.
  • docs: created a QFeatures recap vignette

                      Changes in version 1.3.1                        
    
  • refactor: deprecated rowDataToDF. This function is now replaced by
    QFeatures::rbindRowData.

                       Changes in version 1.3                         
    
                      Changes in version 1.3.0                        
    
  • New devel (Bioc 3.14)
             Changes in version 1.7.3 (2021-10-07)                  
  • Removing more tests attempting to verify that parallelized outputs
    perfectly match their serial counterparts.

               Changes in version 1.7.2 (2021-09-15)                  
    
  • Removing tests checking that sequential and parallel calls to
    scPCA() produce identical outputs when BiocParallel’s SerialParam()
    is used. This due to new handing of random number generation in
    BiocParallel version 1.28.

                   Changes in version 0.99.8                        
  • Included citation for the package

                     Changes in version 0.99.7                        
    
  • Removed global assignment in multiAdaSampling.

                     Changes in version 0.99.6                        
    
  • Revised further to address comments/feedbacks

                     Changes in version 0.99.5                        
    
  • Fixed NEWS to match the version bump

                     Changes in version 0.99.4                        
    
  • Minor change to example in matPC function

                     Changes in version 0.99.3                        
    
  • Correct for any spelling errors in all documentations
  • Revising the package to address the comments from Bioconductor
    review
  • Cleaned the GSE87795 subset data to a SingleCellExperiment object

                     Changes in version 0.99.2                        
    
  • version bump with submission to Bioconductor

                     Changes in version 0.99.1                        
    
  • Cleaning repository to pass BiocCheck

                     Changes in version 0.99.0                        
    
  • Initial submission for Bioconductor
  • Code formats/documentations have been revised to meet Bioconductor
    requirements

                      Changes in version 0.1.1                        
    
  • Significant updates and addition to the documentations
  • Major changes to code writing style to comply with BioC
  • Updated example data
                    Changes in version 0.1.0                        
  • New package scShapes, for identifying and modeling distribution
    shapes of single-cell RNA sequencing data.
                    Changes in version 2.4.0                        
  • Regularizer parameter (L2_A/L1_A) was added in cellCellDecomp()
    (“ntd”, “ntd2”).

  • Multilinear CX Decompotision was added in cellCellDecomp() (“cx”).

  • convertNCBIGeneID is removed.

  • The vignettes were modified.

  • Support of LRBase.XXX.eg.db-type packages is completely deprecated

                   Changes in version 0.99.00                       
  • Added a NEWS.md file to track changes to the package.
                    Changes in version 1.5.1                        
  • Prepare for release

                      Changes in version 1.4.1                        
    
  • Prepare for release

                   Changes in version 1.15.1                        
  • import yulab.utils (2021-08-20, Fri)
  • mv seqdiff and simplot to ggmsa package
                   Changes in version 1.11.2                        

New functionality

  • Changes in version 1.11.2 (2021-09-14) Update the DESCRIPTION
    file, vignettes file and the NEWS file.
             Changes in version 1.7.3 (2021-08-24)                  
  • Improved get_targets function by supporting different output
    format.

               Changes in version 1.7.2 (2021-06-14)                  
    
  • Supported automatic downloads of ExperimentHub cached files.

                   Changes in version 1.19.1                        
  • migrate to PMCMRplus package
             Changes in version 2.3.2 (2021-10-24)                  
  • Added summary table into the cellQC report
  • Improved formatting in QC report
  • Added functions getDEGTopTable() & plotBatchCorrCompare()
  • Other refactors and bug fixes

               Changes in version 2.3.1 (2021-10-15)                  
    
  • Several bug fixes

               Changes in version 2.2.2 (2021-10-10)                  
    
  • Several enhancements, refactors, and bug fixes to the UI
  • Refactor documentation and pkgdown site
  • Added tutorials for R console analysis
  • Updates to the UMAP generation in the SCTK-QC pipeline
  • Addition of VAM to Pathway prediction tab
  • Bug fix to the mitochondrial gene set functions
                    Changes in version 1.9.4                        
  • Fix: special case when tree root has more than one lineage path

                      Changes in version 1.9.3                        
    
  • Fix: invalid parallel mutations at divergent node.

  • Update DESCRIPTION, README and vignettes.

                      Changes in version 1.9.2                        
    
  • Allow partially plot ‘lineagePath’.

  • Improved ‘plotMutSites’ function for ‘lineagePath’.

                      Changes in version 1.9.1                        
    
  • Add ‘useSites’ argument to ‘setSiteNumbering’ function.

  • First ‘stable’ path as default ‘lineagePath’.

  • Enable plot functions for ‘parallelSites’.

             Changes in version 1.4.0 (2021-09-09)                  
  • Add pca, partial_pca, pca_center, pca_scale, pca_dims arguments in
    line with Rtsne::Rtsne
                     Changes in version 1.0                         

Enhancements

  • Released to Bioconductor
  • Adds support for use of BiocSet as a means by which users can bring
    their genesets to – or take them from – sparrow.
  • Improvements to the corplot() functionality contributed by by
    Arkadiusz Gladki (@gladki). Users can specify the size of the text
    reported in the bottom half of the pair plot, and spurious/annoying
    warnings that were produced after a a totally valid call are no
    longer produced.

Breaking Changes from Pre-release

  • First two parameters in ora() function have been swapped so that
    the
    first parameter (x) is the object (data.frame) to run an over
    representation analysis against, and the second parameter is the
    GeneSetDb.
  • scoreSingleSamples no longer drops features in y that are not found
    in the GeneSetDb used for scoring. This was changed so that gsva and
    ssGSEA scores match the scores produced by a normal GSVA::gsva call.
    You can set the drop.unconformed = TRUE to retain the older
    behavior.
             Changes in version 1.3.0 (2021-09-28)                  
  • added S4 wrappers for Seurat and GeoMxSet objects

  • added custom profile matrix generation from single cell data

  • added ~75 profile matrices avaliable to download for human and mouse

             Changes in version 1.3.2 (2021-07-27)                  
             Changes in version 1.99.0 (2021-10-14)                 
  • Implemented overlaying feature: overlay template images in raster
    format with SHMs, where charcoal and transparency options are
    provided.

  • Implemented Spatial Single Cell functionality: co-visualize single
    cells and bulk tissues by placing single-cell embedding plots (PCA,
    tSNE, UMAP) and SHMs side by side, cell cluster assignments are
    defined in the app or provided by users, in dimensionality plots
    shapes are not restricted to 6, etc.

  • Spatial enrichment was synced to R command line.

  • Implemented Sigle and Multiple search mode for gene IDs.

                   Changes in version 0.99.7                        
  • added direct support for GenomicInteractions objects

  • improved vignettes

  • removed biomaRt requests

  • added support for R 4.1

  • added ‘Transcription’ Bioconductor Views annotation

                     Changes in version 0.99.0                        
    
  • initial pre-release

                     Changes in version 1.3                         

Changes in 1.3.11

  • Fix error message in setBackend (issue #217).

Changes in 1.3.10

  • Fix bug in plotSpectra and plotSpectraMirror that would cause an
    error if the number of peaks in a spectrum was 1 and labels were
    provided.

Changes in 1.3.9

  • New features: joinSpectraData() now check for duplicated keys in x
    (throws an error) and y (thows a warning).

Changes in 1.3.8

  • New features: plotMzDelta() function to M/Z delta QC (ported from
    MSnbase).

Changes in 1.3.7

  • Add fix from MSnbase (issue #170) to Spectra: on macOS require
    reading also the spectrum header before reading the peaks data.

Changes in 1.3.6

  • Documentation updates for combineSpectra and combinePeaks.

Changes in 1.3.5

  • filterMzValues supports also removing peaks matching specified m/z
    values (issue #209).

Changes in 1.3.4

  • Add list of additional R packages and repositories providing
    MsBackend backends to the vignette.

Changes in 1.3.3

  • Move generics for bin and compareSpectra to ProtGenerics.

Changes in 1.3.2

  • Add parameter f to filterPrecursorScan to fix issue #194.

Changes in 1.3.1

  • Add estimatePrecursorIntensity function (issue #202).
                    Changes in version 0.1.0                        
  • Initial addition of functions and tests
             Changes in version 1.18.0 (2021-10-27)                 
  • Updates to the splatPop simulation (from Christina Azodi)

• Added functionality to simulate directly from empirical
values

• Added eqtl.coreg parameter to splatPop

• Fixed a bug where too many cells were simulated in splatPop
with multiple batches

• Fixed duplicate cell names in splatPopSimulate

                    Changes in version 1.0.3                        
                     Changes in version 2.0                         

NEW FEATURES

  • New GUI
    o Mouse Hover for help information
    o .log file

  • New Signal correction
    o Combat for QC-free Signal correction
    o QC-RFSC methods for metabolomics and proteomics data

  • New feature slection
    o Random Forest and the Permutation based variable importance
    measures
    o new MDSplot for Random Forest
    o P-value based importance plot

  • New data preprocessing
    o PQN/SUM/none normalization
    o center/none Scaling method

                    Changes in version 1.5.3                        
                    Changes in version 1.5.7                        
  • improve NA handling in fold_change computations

                      Changes in version 1.5.5                        
    
  • change t-test outputs to data.frame

  • fix NA bug in feature_boxplot chart

  • use new ontology system in place of stato

                      Changes in version 1.5.2                        
    
  • add outputs to auto-generated documentation

  • fix fold change threshold using median (#56)

  • add fold change using means (#57)

  • HSD param “unbalanced” is no longer ignored

                      Changes in version 1.5.1                        
    
  • fixed broken paired tests

                      Changes in version 1.4.2                        
    
  • fix fold change threshold using median (#56)

  • HSD param “unbalanced” is no longer ignored

                      Changes in version 1.4.1                        
    
  • fixed broken paired tests

                   Changes in version 1.24.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

  • Check the assay dimnames at SummarizedExperiment construction time:
    The SummarizedExperiment() constructor function now raises an error
    if one of the supplied assays has rownames and/or colnames that don’t
    match those of the SummarizedExperiment object to construct.
             Changes in version 0.99.6 (2021-10-25)                 
  • Fixed text for consistency in package name

               Changes in version 0.99.5 (2021-10-21)                 
    
  • Fixed text for consistency in package name

               Changes in version 0.99.4 (2021-10-12)                 
    
               Changes in version 0.99.3 (2021-10-11)                 
    
  • Fixed .gitignore file to fix build error

               Changes in version 0.99.2 (2021-09-14)                 
    
  • Fixed bug in script

               Changes in version 0.99.0 (2021-08-24)                 
    
  • Submitted to Bioconductor

             Changes in version 0.99.0 (2021-04-28)                 
  • Submitted to BioConductor
             Changes in version 0.99.0 (2021-04-28)                 
  • Submitted to BioConductor
           Changes in version 2021-07-02 (2021-07-02)               

Changes:

                    Changes in version 2.17                         

Changes in version 2.17.3

  • put commented code chunk back in

Changes in version 2.17.2

Changes in version 2.17.1

  • Update Laurent’s email address
                    Changes in version 1.5.4                        
  • Added the function SubSetPairs that allows for easy trimming of
    predicted pairs based on conflicting predictions and / or prediction
    statistics.
  • Added the function EstimageGenomeRearrangements that generates
    rearrangement scenarios of large scale genomic events using the
    double cut and join model.

                      Changes in version 1.5.3                        
    
  • Added the function SequenceSimilarity and made improvements to
    runtime in DisjointSet.

                      Changes in version 1.4.1                        
    
  • Fixed a small bug in consensus scores in PairSummaries where
    features facing on different strands had their score computed
    incorrectly.
                   Changes in version 1.3.15                        

New Feature

  • In workflow module, workflow designer (step 3), added two new
    parameter when creating a new step, mandatory and place of
    execution. These are new features added in systemPipeR 1.27.27.

Minor Change

  • Bump version requirements of spsComps, systemPipeR, systemPipeRdata

  • In global.R, now use spsOption with the .list argument to set up
    options instead of the base options function.

  • Replace includeMardown() by markdown(readLines()) so we don’t need
    additional {markdown} package as dependency.

Bug Fix

New Feature

  • Add code display buttons to most plots that will show code to
    reproduce the plot.

  • Add two args buttonType and placeholder to dynamicFile, now users
    can specify what bootstrap color the button is and use placeholder
    to specify initial text on the upload bar.

  • Enhanced the original shiny fileInput, now users can also
    specify icon and button bootstrap colors for “server” mode in
    dynamicFile.

Major Change

  • Redesign of a few steps in Workflow module. The new version of
    {systemPipeR} fundamentally changed how the workflow will be run. To
    sync to this new version, WF module has to been redesigned. Major
    change happens on workflow step selection. This requires users to
    install systemPipeR > 1.27.10

  • New methods to initiate the WF project

  • New workflow plot

  • New step selection mechanism

  • New step editing functionalities

Minor Change

  • For RNAseq module, the dendrogram plot library changed from
    {ggtree}
    package to {ape}. {ggtree} is not very compatible with Shiny under
    current version. Plot cannot be created, always error, but no error
    outside Shiny. An issue has submitted to Shiny on Github. We may
    switch back to ggtree when this is fixed.
  • Small UI optimization for RNAseq module.
  • Fixed some typo in different tabs.

Bug Fix

  • #85 fix dynamicFile icon not working

  • Also add some icon validation code

  • Fix the admin server tabs get loaded twice. Added a flag to prevent
    this from happening.

                      Changes in version 1.3.0                        
    
  • Update version number to 1.3.0 per Bioconductor regulation.

                    Changes in version 0.99                         

NEW FEATURES

  • initial release. The main functions are ggsplitnet and ggevonet to
    visualize split (or implicit) networks (unrooted, undirected) and
    explicit
    networks (rooted, directed) with reticulations.
             Changes in version 1.5.1 (2021-08-27)                  
                   Changes in version 1.50.0                        

NEW FEATURES

  • FindAllPeaks: Allow for asymmetric RT deviations. Formerly, the
    window
    search parameter was plus o minus a tolerance; now it can be
    different on either
    side of the expected RT.

  • ncdf4_convert_from_path: New flag to convert CDF files recursively.

  • checkRimLim: show multiple samples at the same time, as opposed to a
    single sample in previous versions.

BUG FIXES

  • Make sure that the assertion that checks for NULL or NA is operating
    in a
    scalar. For vectors use another assertion.

  • Code clean-up. Remove unneeded files.

                    Changes in version 1.5.0                        
  • 68 signatures currently available

Bug Fixes

  • Fixed incorrect names of signatures in Tbcommon and
    common_sigAnnotData objects

Major Changes

  • Added Zimmer_RES_3, Gong_OD_4, Bloom_RES_268, and Bloom_RES_558
  • Added Sivakumaran_11 and Mendelsoh_RISK_11 signatures
  • Added Estevez_133, Estevez_259, LauxdaCosta_OD_3, and Maertzdorf_15
    signatures to the package
  • Added Chen_HIV_4, Gliddon_HIV_3, Gliddon_2_OD_4, Kulkarni_HIV_2,
    and
    Heycken_FAIL_22 signatures
  • Added a COVIDsignatures object to the package that can be used to
    profile COVID-19 gene transcript signatures, thanks to collaborator
    Dylan Sheerin (WEHI)
  • Added functions to evaluate some signatures using their original
    models from Johnson lab member Xutao Wang

Minor Changes

  • Added mention of COVIDsignatures object to main vignette and
    website
  • Included the OG models tutorial on website (Xutao Wang)
  • Added addTBsignature() to more easily facilitate updating
    signatures
    in package
  • Added pROC option to obtain confidence intervals on AUC values as
    part of code{tableAUC()}
  • Added citation for newly published paper
                   Changes in version 2.21.1                        
                   Changes in version 1.14.0                        

Minor changes and bug fixes

  • UUIDtoBarcode with the from_type = “file_id” argument now returns
    the IDs in the proper order when more than one UUID is input.
  • Update makeGRangesListFromCopyNumber examples with new names from
    API e.g., ‘associated_entities.entity_submitter_id’
                    Changes in version 1.6.1                        
  • Correct the citation error.
                    Changes in version 1.15                         
  • New version for Bioc 3.15 (devel)

Changes in version 1.15.1

                    Changes in version 1.3.4                        
  • Fix bug in tests when run on Windows due to uninherited namespace
    imports for testthat::context and testthat::expect_equal inside a
    bplapply call

                      Changes in version 1.3.3                        
    
  • Debugging BioC build ERROR caused by updates to CoreGx

                      Changes in version 1.3.2                        
    
  • Fix a bug in computeLimmaDiffExpr where subsetting a ToxicoSet
    doesn’t subset the protocolData of a SummarizedExperiment, causing
    coercing to an ExpressionSet inside the function to fail
  • For now just deleting protocolData from the metadata of the
    SummarizedExperiment, but will eventually need to be fixed upstream
    in ORCESTRA

                      Changes in version 1.3.1                        
    
  • Molecular profile data is now subset in test to keep package size
    down

                      Changes in version 1.3.0                        
    
  • Spring 2021 Bioconductor release!
                   Changes in version 1.29.8                        
  • Fix the a typo in read hic data.

                     Changes in version 1.29.7                        
    
  • Fix the bug ‘breaks’ are not unique

                     Changes in version 1.29.6                        
    
  • Add smooth curve to the tracks.

                     Changes in version 1.29.5                        
    
  • Improve gene track plots.

                     Changes in version 1.29.4                        
    
  • Fix the issue for auto-rescale lolliplot by emphasizing exon region
    when there are continues exons.

                     Changes in version 1.29.3                        
    
  • Add the possibility to lolliplot to emphasize exon or intron region.

                     Changes in version 1.29.2                        
    
  • Fix the yaxis when user supplied yaxis is greater than max scores.

                     Changes in version 1.29.1                        
    
  • Update documentation lolliplot for rescale parameter.

                     Changes in version 0.1                         
                    Changes in version 1.2.2                        

BUG FIX

SIGNIFICANT USER-VISIBLE CHANGES

  • There was a bug in version 1.2.0 with the release update of
    Bioconductor.
    That’s fixed in 1.2.1.
                    Changes in version 1.5.1                        
  • Object transformation functions condensed into the
    treeAndLeaf function, to be made automatically [2020-08-24].

  • TreeAndLeaf function became more automated.

  • The igraph object manipulation was upgraded, through the use of
    RedeR functions.

                   Changes in version 1.17.2                        
             Changes in version 0.1.0 (2021-07-03)                  
  • Submitted to Bioconductor
             Changes in version 0.99.0 (2021-08-15)                 
  • Submitted to Bioconductor
  • Added a NEWS.md file to track changes to the package.
             Changes in version 1.19.1 (2021-08-30)                 

Bug fix

                   Changes in version 0.99.0                        

NEW FEATURES

  • Staged for Bioconductor submission.

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

  • None.

                      Changes in version 0.3.2                        
    

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

  • None.

                      Changes in version 0.3.1                        
    

NEW FEATURES

  • Compressed outputs.
  • Tests for proper handling of transitive merging. Overlaps that
    merge
    A -> B and B -> C, but not A -> C, will output A -> C and B -> C.
    That is, transitivity is applied and the final output will always
    use the distal most transcript in a chain as the final output.

SIGNIFICANT USER-VISIBLE CHANGES

  • All export*() methods now include automatic detection of .gz
    filenames, which toggles the use of compressed (gzip) exports.

BUG FIXES

  • None.

                      Changes in version 0.3.0                        
    

NEW FEATURES

  • Merge table generation and exporting.

SIGNIFICANT USER-VISIBLE CHANGES

  • Adds generateMergeTable() and exportMergeTable() for creating a
    merge table for transcripts that are not separated by a thresholded
    distance. Such files can be used by transcript quantification tools
    to specify what transcripts should be merged.

BUG FIXES

  • None.

                      Changes in version 0.2.2                        
    

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

  • Added a NEWS.md file to track changes to the package.
  • Provide more control over parallel execution.

SIGNIFICANT USER-VISIBLE CHANGES

  • The truncateTxome() method includes an optional BPPARAM with which
    users can pass a specific BiocParallelParam. If not provided, it
    will respect the result of BiocParallel::bpparam(), which can be
    globally set using BiocParallel::register().

BUG FIXES

  • None.

                      Changes in version 0.2.0                        
    

NEW FEATURES

  • Adds deduplication behavior. Note that deduplication does not
    exclude transcripts from different genes.

SIGNIFICANT USER-VISIBLE CHANGES

  • The truncateTxome() method now deduplicates transcripts spanning
    identical ranges after truncation.

BUG FIXES

                   Changes in version 1.12.0                        

NEW FEATURES

  • New function, sequence_complexity(): Using either the
    Wootton-Federhen,
    Trifonov, or DUST algorithms, calculate sequence complexity in
    sliding
    windows. A version for small arbitrary strings is also provided:
    calc_complexity().

  • New function, mask_ranges(): Similarly to mask_seqs(), mask specific
    positions in a XStringSet object by replacing the letters with a
    specific
    filler character.

  • New function, motif_range(): Get the min/max range of possible
    logodds
    scores for a motif.

  • New function, calc_windows(): Utility function for calculating
    coordinates for sliding windows.

  • New function, window_string(): Utility function for retrieving
    sliding
    windows in a string.

  • New function, slide_fun(): Utility function which wraps
    window_string()
    and vapply() together.

  • motif_pvalue(method): P-values and scores can now be calculated
    dynamically instead of exhaustively, substantially increasing both
    speed
    and accuracy for bigger jobs. The previous exhaustive method can
    still be
    used however, as the dynamic method does not allow non-finite values
    and
    thus must be pseudocount-adjusted.

  • scan_sequences(calc.pvals, calc.qvals, motif_pvalue.method,
    calc.qvals.method): The calc.pvals argument defaults to TRUE.
    The P-value calculation method now defaults to dynamic P-values (the
    previous method was an exhaustive calculation), though this can be
    changed via motif_pvalue.method. Additionally, adjusted P-values can
    be
    calculated as either BH, FDR or a Bonferroni-adjusted P-value. More
    details can be found in the Sequence Searches vignette.

  • write_homer(threshold, threshold.type): Finer control over the final
    motif logodds threshold included with the written motif is now
    available, using the style of argument parsing from scan_sequences().
    The previous logodds_threshold argument is now deprecated and set to
    NULL, but if set (e.g. an older script is being re-run) then the old
    behaviour of write_homer() will be used.

MINOR CHANGES

  • New global option, options(pseudocount.warning): Disable the message
    printed when a motif is pseudocount-adjusted.

  • Slight performance gains in get_bkg() window code.

  • motif_pvalue(): Clarify that, indeed, background probabilities are
    taken
    into account when calculating P-values from score inputs. The
    background
    adjustment takes place during the initial conversion to PWM.

  • motif_pvalue(): When bkg.probs are provided, use those when
    converting to
    a PWM.

  • scan_sequences(): The default threshold is now 0.0001 (using
    threshold.type = “pvalue”).

  • The axis text in view_motifs() is now black instead of grey.

  • create_motif(): When a named background vector is provided, it is
    sorted according to the alphabet characters.

  • scan_sequences(): Check that the sequences aren’t shorter than the
    motifs.

  • print.universalmotif_df: Changed warning message when subsetting to
    an
    incomplete universalmotif_df object. Also added a way to turn off
    informative messages/warnings via the boolean
    universalmotif_df.warning
    global option.

  • Miscellaneous changes and additions to the vignettes and various
    function manual pages.

                     Changes in version 1.10.2                        
    

BUG FIXES

BUG FIXES

  • Restore temporarily disabled ggtree(layout=”daylight”) example in the
    MotifComparisonAndPvalues.Rmd vignette, as tidytree is now patched.

  • Fixed some awkwardness in view_motifs() panel spacing and title
    justification.

             Changes in version 0.99.0 (2021-06-07)                 
  • submission to Bioconductor
                    Changes in version 1.3.1                        
  • Add typing_extensions to environment
                 Changes in version 0.0.0.9000                      
  • Added a NEWS.md file to track changes to the package.
                     Changes in version 1.7                         
  • Ensembl2GO() biomart update
                    Changes in version 1.2.0                        
  • Added weighting to text-mining analysis. Word clouds can now
    incorporate statistics.
  • Network plotting now performed using ggraph.
  • Removal of excessive warnings produced when performing text-mining.
  • Added PPI exploration of clusters
                    Changes in version 1.5.1                        
  • weitrix_sd_confects now has an option to drop the assumption of
    normally distributed weighted residuals.
             Changes in version 1.1.3 (2021-10-05)                  
  • The workflow calculates Protein-Protein Interaction weights and
    scores genes
  • Database knowledge is automatically fetched from OmniPath, Gene
    Ontology and Human Phenotype Ontology
  • Submitted to Bioconductor
                   Changes in version 3.15.5                        
  • Disable testing on windows i386, providing some speedup

  • Disable parallel processing on Windows, causing an issue in testthat
    on BioC build check

                     Changes in version 3.15.4                        
    
  • Fix in plot with type = "XIC" to plot an empty plot if no data is
    present.

  • Skip re-indexing of peaks to features if not necessary. This results
    in
    performance improvements for MS1 only data.

                     Changes in version 3.15.3                        
    
  • Add manualFeatures allowing to manually define and add features to
    an
    XCMSnExp object.

  • Add plotChromatogramsOverlay function to support plotting of
    multiple EICs
    from the same sample into the same plot (eventually stacked).

  • Add feature grouping by EIC similarity: EicSimilarityParam.

  • Import compareChromatograms from MSnbase.

  • Add feature grouping by similar retention time: `SimilarRtimeParams.

  • Add feature grouping by similarity of feature abundances across
    samples:
    AbundanceSimilarityParam.

  • Add feature grouping methodology based on MsFeatures.

                     Changes in version 3.15.2                        
    
  • Fix LC-MS/MS vignette.

                     Changes in version 3.15.1                        
    
  • Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus.

                    Changes in version 1.4.0                        
  • Add arguments to control how slots are converted in
    AnnData2SCE() and SCE2AnnData(). Each slot can now be fully
    converted, skipped entirely or only selected items converted.

  • Add support for converting the raw slot to an altExp in
    AnnData2SCE()

  • Add recursive conversion of lists in AnnData2SCE()

  • Add progress messages to various functions. These can be
    controlled by function arguments or a global variable.

  • Add long tests for various public datasets. This should help to
    make the package more robust

  • Fix bug in converting dgRMatrix sparse matrices

  • Correctly handle DataFrame objects stored in adata.obsm

             Changes in version 1.7.1 (2021-06-18)                  
  • Added rmarkdown to Suggests in DESCRIPTION to resolve changes in
    knitr
                    Changes in version 1.0.2                        

NEW FEATURES

  • Updated the vignettes.

                      Changes in version 1.0.1                        
    

NEW FEATURES

  • Modified the file format from Rda to rds.
             Changes in version 1.9.1 (2021-06-18)                  
  • Added rmarkdown to Suggests in DESCRIPTION to resolve changes in
    knitr
                    Changes in version 3.2.0                        
  • The curatedMetagenomicData() function now has a rownames argument:

  • “long”, the default character string derived from MetaPhlAn3

  • “short”, the NCBI Taxonomy species name from the CHOCOPhlAn
    database

  • “short” row names are validated against NCBI Taxonomy with
    taxize

  • “NCBI”, the NCBI Taxonomy ID from the CHOCOPhlAn database

  • “NCBI” row names are validated against NCBI Taxonomy with
    taxize

  • rowData becomes NCBI Taxonomy ID numbers instead of taxa
    names

  • The sparse matrix data structure was switched from dgTMatrix to
    dgCMatrix

  • A few studies were reprocessed because of a minor error related to
    MetaPhlAn3

  • Changes inside the package were made to address bugs discovered by
    users

  • The combined_metadata object has been removed

             Changes in version 0.99.4 (2021-10-18)                 
  • Update vignette output

  • Edit DESCRIPTION file

               Changes in version 0.99.3 (2021-10-07)                 
    
  • Remove analysis/graphical functions from the master branch

  • Accepted by Bioconductor

               Changes in version 0.99.2 (2021-09-24)                 
    
  • Remove cached files from git history

  • Modify packages based on reviewer’s comment

               Changes in version 0.99.0 (2021-09-16)                 
    
  • The curatedTBData package collects 49 transcriptomic studies

  • Package vignette is updated to Rmd syntax and uses BiocStyle

  • All data is reprocessed in R (v4.1)

  • Move all data to ExperimentHub

  • Added a NEWS.md file to track changes to the package

  • Submitted to Bioconductor

            Changes in version 1.7.1                  
  • 21Q3 data added for crispr, copyNumber, TPM, mutationCalls and
    metadata datasets. Newer versions for the other datasets were
    not released.

  • CERES CRISPR data has been deprecated and has been replaced with
    Chronos CRISPR dependency in 21Q3 and all future releases. For
    more information, see:
    cancerdatascience.org/blog/posts/ceres-chronos/

             Changes in version 1.5.2 (2021-10-13)                  
  • Daniel Dimitrov is assigned as the new maintainer

               Changes in version 1.4.2 (2021-10-08)                  
    
  • Fixed lazy data warning

  • Improved test coverage

               Changes in version 1.4.1 (2021-05-25)                  
    
  • Rebuild all regulons

  • Fixed ambiguously mode of regulation in mouse regulons

                   Changes in version 0.99.0                        
  • All set for the Bioconductor submission!

                      Changes in version 0.9.0                        
    
  • Getting ready for the submission to Bioconductor

  • Added a NEWS.md file to track changes to the package.

             Changes in version 1.1.1 (2021-05-25)                  
  • Added documentation (dataset list in README, print out examples in
    help pages)
                    Changes in version 3.13                         
  • Add MSigDB datasets

  • Add note in vignettes

             Changes in version 1.1.5 (2021-09-08)                  
  • GrieneisenTS data added

  • HintikkaXO data added

  • Minor fixes

                    Changes in version 1.2.0                        
  • added MSigDB v7.4

  • removed gene-sets from the “archived” category from all collections

  • removed direct object referencing functions (e.g.
    msigdb.v7.2.hs.SYM()). Objects should be retrieved using the
    getMsigdb() function only or by querying the ExperimentHub

  • added IMEx PPI data

                   Changes in version 1.23.4                        
  • temporarily disable all vignettes until CAMERA issue is fixed

                     Changes in version 1.23.2                        
    
  • switch to mzML files in the ISA-Tab metadata

  • temporarily disable the vignette for the old xcms interface causing a
    build failure

                     Changes in version 1.23.1                        
    
  • add mzML versions of mzData files converted by OpenMS FileConverter

             Changes in version 0.99.3 (2021-09-27)                 
  • Now uses BiocFileCache to store a copy of ExperimentHub resources.
    Allows for faster subsequent recalls

               Changes in version 0.99.0 (2021-09-17)                 
    
  • Submitted to Bioconductor

             Changes in version 1.1.1 (2021-03-05)                  
                   Changes in version 1.31.1                        
  • Fix mztab file name (required for new rpx)

                     Changes in version 1.31.0                        
    
  • New version for Bioc 3.14 (devel)

                   Changes in version 0.99.6                        
                    Changes in version 2.1.1                        
  • Temporarily rolled Ensemble version back to 75 to eliminate numerous
    non-coding transcripts

  • Methylation array information based on the latest manifest file

                      Changes in version 2.1.0                        
    
  • Release May 2021

  • Added annotation for the Mouse Methylation Bead Chip (thanks to Maxi
    Schoenung for his great contribution!).

  • Updated SNP information to GRCm38.p4, the last version available
    through NCBI.

                   Changes in version 0.99.3                        
  • removed usage of paste() function in error handling functions

                     Changes in version 0.99.2                        
    
  • Added NEWS.md file to track changes to the package.

  • Formatted functions to shorten lines

  • Removed usage of T/F in test cases

  • Removed usage of ‘paste’ in condition signals

                     Changes in version 0.99.1                        
    
  • added tests for queryATAC function

  • added new error checking to queryATAC and fetchATAC functions

                    Changes in version 1.1.1                        
  • Added the schoof2021 dataset <2021-10-06>
                    Changes in version 1.6.0                        

New features

  • scMultiome version 1.0.1 provides the 10X format for RNAseq data.

Bug fixes and minor improvements

  • Updates to seqFISH vignette and documentation.

  • Updated to changes in SummarizedExperiment where assayDimnames are
    checked.

  • scNMT defaults to version ‘1.0.0’s QC filtered cells. For unfiltered
    cells see version section in ?scNMT.

                   Changes in version 0.99.9                        
  • Submitting to Bioconductor as a ExperimentHub data package.
                   Changes in version 0.99.1                        
  • Add infoOnly argument to get details about download size

                     Changes in version 0.99.0                        
    
  • Add documentation

  • Prepare for Bioconductor submission

                      Changes in version 0.1.0                        
    
  • Add a NEWS.md file to track changes to the package.

                    Changes in version 1.2.1                        
  • Added a summary column to the metadata table and SingleCellExperiment
    metadata
                    Changes in version 1.0.0                        
  • tuberculosis is now available in Bioconductor Release 3.14
                   Changes in version 0.99.4                        
  • Updated workflow image

                     Changes in version 0.99.3                        
    
  • Removed empty DCC file from example dataset
  • Adjusted QC plotting histogram function to remove user-defined
    limits

                     Changes in version 0.99.2                        
    
  • Version update for bioconductor build review

                     Changes in version 0.99.1                        
    

NEW FEATURES

  • Added a NEWS.md file to track changes to the package
  • Removed DESCRIPTION and Namespace conflicts
  • Updated styling of vignette (GeomxTools_RNA-NGS_Analysis.Rmd) to fit with BioC

No new NEWS to report

Forty seven software packages were removed from this release (after being deprecated
in Bioc 3.13):
AffyExpress, affyQCReport, AnnotationFuncs, ArrayTools, bigmemoryExtras,
BiocCaseStudies, CancerMutationAnalysis, ChIPSeqSpike, CompGO, CoRegFlux,
CrossICC, cytofast, DBChIP, dexus, EasyqpcR, EDDA, eisa, ELBOW, ExpressionView,
FlowRepositoryR, genoset, HCABrowser, HCAExplorer, HCAMatrixBrowser, Imetagene,
mdgsa, metagenomeFeatures, methyAnalysis, MSEADbi, OutlierD,
pcot2, PCpheno, Polyfit, POST, RchyOptimyx, RDAVIDWebService, RNAither,
RNAprobR, rnaSeqMap, SAGx, samExploreR, seqplots, simulatorZ, SSPA, ToPASeq,
XBSeq, yaqcaffy

Please note: CexoR and IntramiRExploreR, previously announced as deprecated in
3.13, fixed their packages and remained in Bioconductor.

Twenty three software packages are deprecated in this release and will be removed in Bioc 3.15:
affyPara, ALPS, alsace, BrainStars, destiny, dualKS, ENCODExplorer,
ENVISIONQuery, FindMyFriends, GeneAnswers, gramm4R, KEGGprofile, MouseFM,
MSGFgui, MSGFplus, MSstatsTMTPTM, PanVizGenerator, predictionet, RGalaxy,
scClassifR, slinky, SRGnet, SwimR

Eleven experimental data packages were removed this release (after being
deprecated in BioC 3.13):
ceu1kg, ceu1kgv, ceuhm3, cgdv17, dsQTL, facsDorit, gskb, hmyriB36, JctSeqData,
MAQCsubsetAFX, yri1kgv

Five experimental data packages are deprecated in this release and will be
removed in Bioc 3.15:
ABAData, brainImageRdata, PCHiCdata, RITANdata, tcgaWGBSData.hg19

Eighty seven annotation packages were removed from this release (after being deprecated
in Bioc 3.13):
12 LRBase.XXX.eg.db packages (replaced with AHLRBaseDbs),
MafDb.gnomAD.r3.0.GRCh38, MafH5.gnomAD.r3.0.GRCh38, 73 MeSH.XXX.eg.db packages
(replaced with AHMeSHDbs)

One annotation package was deprecated in this release and will be removed in
Bioc 3.15:
org.Pf.plasmo.db

One workflow package was removed from this release (after being deprecated
in Bioc 3.13):
eQTL

No workflow packages were deprecated in this release.

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