Bioconductor – Bioconductor 3.14 Released – Open Source Biology & Genetics Interest Group

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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.

To update to or install Bioconductor 3.14:

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

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

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

(v 1.27.10) Typo in coercion to SerialParam when only a single worker
specified. github.com/Bioconductor/BiocParallel/issues/151

                   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

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

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

                    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

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

goSlim() does not truncate Terms
(github.com/Bioconductor/GSEABase/issues/5)

                    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

Sync API with matrixStats v0.60.1.

                  Changes in version 1.5.2

Sync API with matrixStats v0.60.0.

                  Changes in version 1.5.1

Fix problem with function environment of fallback mechanism
(<URL:
github.com/Bioconductor/MatrixGenerics/issues/25> and
<URL: github.com/Bioconductor/MatrixGenerics/pull/26>).
Make sure that packages can use MatrixGenerics with the ::
notation to call functions from sparseMatrixStats and
DelayedMatrixStats.

             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

XCMS 3 compatability update (M-R-JONES)
github.com/computational-metabolomics/msPurity/pull/91

                 Changes in version 1.19.1

Bug fix for flagRemove (full width was not calculated as expected)

                    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

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

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

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

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

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

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 bothfittingEval’ 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

Fix a bug in geo_info() for reading files on Windows where a
trailing r was added to all variables.
Avoid the implicit list embedding of S4 objects is deprecated
warning that was noted at
github.com/leekgroup/recount/runs/3286046827?check_suite_focus=true#step:20:1417.

                    Changes in version 1.3.9

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

rowRanges(rse_gene)$score is now rowRanges(rse_gene)$bp_length to
make it easier to use recount::getTPM() and recount::getRPKM() with
recount3 objects. Resolves
github.com/LieberInstitute/recount3/issues/4.

BUG FIXES

Updated read_metadata() based on
github.com/LieberInstitute/recount3/issues/5. The empty
metadata will be dropped with a warning in situations like that.

                    Changes in version 1.3.1

Change the email from w.tao-2@umcturecht.nl to
weiyangtao1513@gmail.com

             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

Add rmarkdown to Suggests:; see
github.com/yihui/knitr/issues/1864 for details [2021-07-27].

                    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

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

RLHub provides convenient access to the processed datasets
within RLBase. A full step-by-step protocol for replicating RLHub is
found here github.com/Bishop-Laboratory/RLBase-data

                    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.

Bioconductor – Bioconductor 3.14 Released

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