Tag: testthat

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

Hi folks! I’ve encountered an intriguing issue while conducting a package installation process. Currently, I’m working on R version 4.2.1 within the Posit Workbench 2023.03.1+446.pro1, “Cherry Blossom” environment. I’ve developed a package named APIUtilizeR and subsequently uploaded it to our internal POSIT Package Manager. Within the DESCRIPTION file of this…

DOI: 10.18129/B9.bioc.dcanr     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see dcanr. Differential co-expression/association network analysis Bioconductor version: 3.12 Methods and an evaluation framework for the inference of differential co-expression/association networks. Author: Dharmesh D. Bhuva [aut, cre] Maintainer: Dharmesh D. Bhuva <bhuva.d…

DOI: 10.18129/B9.bioc.chimeraviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chimeraviz. Visualization tools for gene fusions Bioconductor version: 3.12 chimeraviz manages data from fusion gene finders and provides useful visualization tools. Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M….

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

Article Summary Box Mastering the RStudio interface goes beyond basic navigation, involving strategic use of panes and shortcuts to streamline the coding process. Effective script organization significantly impacts readability and maintenance, emphasizing the role of modular structuring and clear documentation. In debugging and error handling, advanced techniques like conditional breakpoints…

Article Summary Box Customizing the RStudio Environment significantly boosts productivity, with options like project-specific settings and theme personalization enhancing the user experience. Advanced ggplot2 Techniques in data visualization offer a blend of aesthetics and functionality, enabling the creation of visually striking and informative plots. Efficient Data Management strategies in RStudio,…

DOI: 10.18129/B9.bioc.pgxRpi   This is the development version of pgxRpi; to use it, please install the devel version of Bioconductor. R wrapper for Progenetix Bioconductor version: Development (3.19) The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a…

DOI: 10.18129/B9.bioc.DropletUtils     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DropletUtils. Utilities for Handling Single-Cell Droplet Data Bioconductor version: 3.15 Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data…

DOI: 10.18129/B9.bioc.epivizrChart     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see epivizrChart. R interface to epiviz web components Bioconductor version: 3.14 This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used…

DOI: 10.18129/B9.bioc.semisup   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see semisup. Semi-Supervised Mixture Model Bioconductor version: 3.16 Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis…

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DOI: 10.18129/B9.bioc.crisprBase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see crisprBase. Base functions and classes for CRISPR gRNA design Bioconductor version: 3.16 Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to…

running R (version 4.2.2) and R Studio (version 1.4.1717), with 10GB of memory. trying to install the toolbox “spant” on HPC (high performance computer) cluster, and i get this error > Warning in install.packages: installation of package “spant” had non-zero exit status what am i missing to fix this? i…

DOI: 10.18129/B9.bioc.ptairMS     Pre-processing PTR-TOF-MS Data Bioconductor version: Release (3.13) This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ‘sample by features’ table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for…

R reexports — ggplot2 These objects are imported from other packages. Follow the links below to see their documentation. grid arrow, unit scales alpha . ggplot2::reexports is located in package ggplot2. Please install and load package ggplot2 before use. install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) ggplot(mpg, aes(displ, hwy)) + geom_point(alpha = 0.5,…

DOI: 10.18129/B9.bioc.ggsc   Visualizing Single Cell Data Bioconductor version: Release (3.18) Useful functions to visualize single cell and spatial data. It supports both ‘SingleCellExperiment’ and ‘Seurat’ objects. It also supports visualizing the data using grammar of graphics implemented in ‘ggplot2’. Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]…

R reexports — RSQLite These objects are imported from other packages. Follow the links below to see their documentation. DBI Id . RSQLite::reexports is located in package RSQLite. Please install and load package RSQLite before use. Same Names: ggplot2::reexports, devtools::reexports, tibble::reexports, tidyselect::reexports, purrr::reexports, tidyr::reexports, callr::reexports, testthat::reexports, broom::reexports, sf::reexports, lubridate::reexports, openssl::reexports,…

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

DOI: 10.18129/B9.bioc.scDesign3   A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics Bioconductor version: Release (3.18) We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning…

DOI: 10.18129/B9.bioc.TCGAbiolinks     TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…

DOI: 10.18129/B9.bioc.gatom   Finding an Active Metabolic Module in Atom Transition Network Bioconductor version: Release (3.18) This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module)…

DOI: 10.18129/B9.bioc.gDRtestData   gDRtestData – R data package with testing dose reponse data Bioconductor version: Release (3.18) R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains RDS files with MAE data…

DOI: 10.18129/B9.bioc.phyloseq     Handling and analysis of high-throughput microbiome census data Bioconductor version: Release (3.6) phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Author: Paul J. McMurdie <joey711 at gmail.com>, Susan Holmes <susan at stat.stanford.edu>, with…

DOI: 10.18129/B9.bioc.iCOBRA     Comparison and Visualization of Ranking and Assignment Methods Bioconductor version: Release (3.6) This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results. Author: Charlotte Soneson…

DOI: 10.18129/B9.bioc.cfToolsData   ExperimentHub data for the cfTools package Bioconductor version: Release (3.18) The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with…

DOI: 10.18129/B9.bioc.receptLoss   Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors Bioconductor version: Release (3.18) receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the…

DOI: 10.18129/B9.bioc.gDRcore   Processing functions and interface to process and analyze drug dose-response data Bioconductor version: Release (3.18) This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the…

DOI: 10.18129/B9.bioc.gDRstyle   A package with style requirements for the gDR suite Bioconductor version: Release (3.18) Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make…

DOI: 10.18129/B9.bioc.gDRutils   A package with helper functions for processing drug response data Bioconductor version: Release (3.18) This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many…

DOI: 10.18129/B9.bioc.orthos   `orthos` is an R package for variance decomposition using conditional variational auto-encoders Bioconductor version: Release (3.18) `orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large…

DOI: 10.18129/B9.bioc.EpiTxDb   Storing and accessing epitranscriptomic information using the AnnotationDbi interface Bioconductor version: Release (3.18) EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA…

1. Install r-bioc-scrnaseq package Please follow the step by step instructions below to install r-bioc-scrnaseq package: sudo apt install r-bioc-scrnaseq Copy 2. Uninstall / Remove r-bioc-scrnaseq package This guide let you learn how to uninstall r-bioc-scrnaseq package: sudo apt remove r-bioc-scrnaseq Copy sudo apt autoclean && sudo apt autoremove Copy…

DOI: 10.18129/B9.bioc.ResidualMatrix   Creating a DelayedMatrix of Regression Residuals Bioconductor version: Release (3.18) Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix….

DOI: 10.18129/B9.bioc.plyinteractions   Extending tidy verbs to genomic interactions Bioconductor version: Release (3.18) Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows. Author: Jacques Serizay [aut, cre] Maintainer:…

DOI: 10.18129/B9.bioc.regioneR   This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…

DOI: 10.18129/B9.bioc.megadepth   This is the development version of megadepth; for the stable release version, see megadepth. megadepth: BigWig and BAM related utilities Bioconductor version: Development (3.19) This package provides an R interface to Megadepth by Christopher Wilks available at github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of…

DOI: 10.18129/B9.bioc.simona   Semantic Similarity in Bio-Ontologies Bioconductor version: Release (3.18) The package implements a rich set of methods for semantic similarity analysis on bio-ontologies. They include methods for information contents, similarities between two terms as well as similarities between two groups of terms. It also implements visualizations on DAGs….

DOI: 10.18129/B9.bioc.mariner   This is the development version of mariner; for the stable release version, see mariner. Mariner: Explore the Hi-Cs Bioconductor version: Development (3.19) Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files,…

DOI: 10.18129/B9.bioc.regionalpcs   This is the development version of regionalpcs; for the stable release version, see regionalpcs. Summarizing Regional Methylation with Regional Principal Components Analysis Bioconductor version: Development (3.19) Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic…

DOI: 10.18129/B9.bioc.lemur   Latent Embedding Multivariate Regression Bioconductor version: Release (3.18) Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold…

DOI: 10.18129/B9.bioc.gg4way   4way Plots of Differential Expression Bioconductor version: Release (3.18) 4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the…

DOI: 10.18129/B9.bioc.scider   This is the development version of scider; to use it, please install the devel version of Bioconductor. Spatial cell-type inter-correlation by density in R Bioconductor version: Development (3.18) scider is an user-friendly R package providing functions to model the global density of cells in a slide of…

DOI: 10.18129/B9.bioc.GloScope   This is the development version of GloScope; to use it, please install the devel version of Bioconductor. Population-level Representation on scRNA-Seq data Bioconductor version: Development (3.18) This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic…

DOI: 10.18129/B9.bioc.subSeq     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see subSeq. Subsampling of high-throughput sequencing count data Bioconductor version: 3.9 Subsampling of high throughput sequencing count data for use in experiment design and analysis. Author: David Robinson, John D. Storey, with…

DOI: 10.18129/B9.bioc.dagLogo     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see dagLogo. dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory Bioconductor version: 3.15 Visualize significant conserved amino acid sequence pattern in groups based…

DOI: 10.18129/B9.bioc.nipalsMCIA   This is the development version of nipalsMCIA; to use it, please install the devel version of Bioconductor. Multiple Co-Inertia Analysis via the NIPALS Method Bioconductor version: Development (3.18) Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the…

DOI: 10.18129/B9.bioc.DepInfeR   This is the development version of DepInfeR; for the stable release version, see DepInfeR. Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling Bioconductor version: Development (3.18) DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines…

DOI: 10.18129/B9.bioc.scp     Mass Spectrometry-Based Single-Cell Proteomics Data Analysis Bioconductor version: Release (3.14) Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics (SCP) data. The package is an extension to the ‘QFeatures’ package designed for SCP applications. Author: Christophe Vanderaa [aut, cre] , Laurent Gatto [aut] Maintainer:…

DOI: 10.18129/B9.bioc.easylift   This is the development version of easylift; to use it, please install the devel version of Bioconductor. An R package to perform genomic liftover Bioconductor version: Development (3.18) The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with…

DOI: 10.18129/B9.bioc.ABAEnrichment     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ABAEnrichment. Gene expression enrichment in human brain regions Bioconductor version: 3.11 The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes…

skip_if_lang_is_c <- function() { # See rstudio/learnr#800 # Treat C.UTF-8 locale like C locale (BZ# 16621) # # The wiki page sourceware.org/glibc/wiki/Proposals/C.UTF-8 # says that “Setting LC_ALL=C.UTF-8 will ignore LANGUAGE just like it # does with LC_ALL=C.” This patch implements it. # # The Debian checks use LANG=C.UTF-8, which now…

DOI: 10.18129/B9.bioc.MouseFM   In-silico methods for genetic finemapping in inbred mice Bioconductor version: Release (3.17) This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%). Author: Matthias Munz [aut, cre] , Inken Wohlers [aut] , Hauke Busch [aut] Maintainer: Matthias…

DOI: 10.18129/B9.bioc.ClusterSignificance     The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data Bioconductor version: Release (3.11) The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from…

DOI: 10.18129/B9.bioc.CVE     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CVE. Cancer…

DOI: 10.18129/B9.bioc.mitch   Multi-Contrast Gene Set Enrichment Analysis Bioconductor version: Release (3.17) mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA…

DOI: 10.18129/B9.bioc.scPCA   Sparse Contrastive Principal Component Analysis Bioconductor version: Release (3.17) A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA’s ability to disentangle biological signal from unwanted variation through the use of control…

DOI: 10.18129/B9.bioc.wpm   Well Plate Maker Bioconductor version: Release (3.17) The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of…

DOI: 10.18129/B9.bioc.famat   Functional analysis of metabolic and transcriptomic data Bioconductor version: Release (3.17) Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: – Pathways containing some of the user’s genes and metabolites…

DOI: 10.18129/B9.bioc.blacksheepr   Outlier Analysis for pairwise differential comparison Bioconductor version: Release (3.17) Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics…

DOI: 10.18129/B9.bioc.fastreeR   This is the development version of fastreeR; for the stable release version, see fastreeR. Phylogenetic, Distance and Other Calculations on VCF and Fasta Files Bioconductor version: Development (3.18) Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions…

DOI: 10.18129/B9.bioc.Linnorm   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Linnorm. Linear model and normality based normalization and transformation method (Linnorm) Bioconductor version: 3.16 Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large…

DOI: 10.18129/B9.bioc.magrene   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see magrene. Motif Analysis In Gene Regulatory Networks Bioconductor version: 3.16 magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and…

DOI: 10.18129/B9.bioc.debCAM   Deconvolution by Convex Analysis of Mixtures Bioconductor version: Release (3.17) An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific…

DOI: 10.18129/B9.bioc.bamsignals   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see bamsignals. Extract read count signals from bam files Bioconductor version: 3.16 This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic…

DOI: 10.18129/B9.bioc.missRows   Handling Missing Individuals in Multi-Omics Data Integration Bioconductor version: Release (3.17) The missRows package implements the MI-MFA method to deal with missing individuals (‘biological units’) in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are…

DOI: 10.18129/B9.bioc.crisprVerse   Easily install and load the crisprVerse ecosystem for CRISPR gRNA design Bioconductor version: Release (3.17) The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is…

DOI: 10.18129/B9.bioc.SBGNview   “SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways” Bioconductor version: Release (3.17) SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely…

DOI: 10.18129/B9.bioc.CeTF   Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis Bioconductor version: Release (3.17) This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al….

DOI: 10.18129/B9.bioc.concordexR   Calculate the concordex coefficient Bioconductor version: Release (3.17) Many analysis workflows include approximation of a nearest neighbors graph followed by clustering of the graph structure. The concordex coefficient estimates the concordance between the graph and clustering results. The package ‘concordexR’ is an R implementation of the original…

DOI: 10.18129/B9.bioc.retrofit   RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics Bioconductor version: Release (3.17) RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing…

DOI: 10.18129/B9.bioc.TileDBArray   Using TileDB as a DelayedArray Backend Bioconductor version: Release (3.17) Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances. Author: Aaron Lun [aut, cre], Genentech, Inc….

DOI: 10.18129/B9.bioc.TREG   Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data Bioconductor version: Release (3.17) RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene…

DOI: 10.18129/B9.bioc.granulator   Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data Bioconductor version: Release (3.17) granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface…

DOI: 10.18129/B9.bioc.ppcseq   Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models Bioconductor version: Release (3.17) Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model…

DOI: 10.18129/B9.bioc.fcoex   FCBF-based Co-Expression Networks for Single Cells Bioconductor version: Release (3.17) The fcoex package implements an easy-to use interface to co-expression analysis based on the FCBF (Fast Correlation-Based Filter) algorithm. it was implemented especifically to deal with single-cell data. The modules found can be used to redefine cell…

DOI: 10.18129/B9.bioc.POWSC   Simulation, power evaluation, and sample size recommendation for single cell RNA-seq Bioconductor version: Release (3.17) Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available…

DOI: 10.18129/B9.bioc.biodb   biodb, a library and a development framework for connecting to chemical and biological databases Bioconductor version: Release (3.17) The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, …), as well as to in-house local database files (CSV, SQLite), with easy retrieval…

DOI: 10.18129/B9.bioc.snapcount   R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts Bioconductor version: Release (3.17) snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various…

DOI: 10.18129/B9.bioc.clustifyr   Classifier for Single-cell RNA-seq Using Cell Clusters Bioconductor version: Release (3.17) Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided…

RStudio, a premier integrated development environment (IDE) for R programming language, has established itself as an indispensable tool for statisticians, data scientists and researchers. With its user-friendly interface, it provides powerful coding tools and makes the process of data analysis and visualization simpler and more effective. Its wide range of…

DOI: 10.18129/B9.bioc.SummarizedBenchmark   Classes and methods for performing benchmark comparisons Bioconductor version: Release (3.17) This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the…

DOI: 10.18129/B9.bioc.ToxicoGx   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ToxicoGx. Analysis of Large-Scale Toxico-Genomic Data Bioconductor version: 3.16 Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation,…

DOI: 10.18129/B9.bioc.GSEABase   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GSEABase. Gene set enrichment data structures and methods Bioconductor version: 3.16 This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer:…

DOI: 10.18129/B9.bioc.ceRNAnetsim     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ceRNAnetsim. Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA) Bioconductor version: 3.13 This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one…

DOI: 10.18129/B9.bioc.NxtIRFdata   Data for NxtIRF Bioconductor version: Release (3.17) NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains…

DOI: 10.18129/B9.bioc.demuxmix   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see demuxmix. Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models Bioconductor version: 3.16 A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit…

DOI: 10.18129/B9.bioc.NormalyzerDE   This is the development version of NormalyzerDE; for the stable release version, see NormalyzerDE. Evaluation of normalization methods and calculation of differential expression analysis statistics Bioconductor version: Development (3.18) NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices…

DOI: 10.18129/B9.bioc.GOpro     Find the most characteristic gene ontology terms for groups of human genes Bioconductor version: Release (3.14) Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2…

DOI: 10.18129/B9.bioc.Macarron   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Macarron. Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets Bioconductor version: 3.16 Macarron is a workflow for the prioritization of potentially bioactive metabolites from metabolomics experiments. Prioritization integrates…

DOI: 10.18129/B9.bioc.MDTS     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MDTS. Detection of de novo deletion in targeted sequencing trios Bioconductor version: 3.15 A package for the detection of de novo copy number deletions in targeted sequencing of trios with high…

DOI: 10.18129/B9.bioc.VariantExperiment     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see VariantExperiment. A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend Bioconductor version: 3.12 VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data…

DOI: 10.18129/B9.bioc.gwascat   This is the development version of gwascat; for the stable release version, see gwascat. representing and modeling data in the EMBL-EBI GWAS catalog Bioconductor version: Development (3.18) Represent and model data in the EMBL-EBI GWAS catalog. Author: VJ Carey <stvjc at channing.harvard.edu> Maintainer: VJ Carey <stvjc at…

DOI: 10.18129/B9.bioc.RCX   R package implementing the Cytoscape Exchange (CX) format Bioconductor version: Release (3.17) Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format…

DOI: 10.18129/B9.bioc.autonomics   Generifying and intuifying cross-platform omics analysis Bioconductor version: Release (3.17) This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm. Author: Aditya Bhagwat…

DOI: 10.18129/B9.bioc.MsQuality   MsQuality – Quality metric calculation from Spectra and MsExperiment objects Bioconductor version: Release (3.17) The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards…

Yes, I am aware that there is a previous question of this name from 9 years ago. The answer is not usable. (RStudio “Source on Save” button missing) My “Source on Save” checkbox is not available for one (but not several other) R scripts. This is the checkbox that is…

DOI: 10.18129/B9.bioc.BioNAR   Biological Network Analysis in R Bioconductor version: Release (3.17) the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of…

DOI: 10.18129/B9.bioc.rmspc   Multiple Sample Peak Calling Bioconductor version: Release (3.17) 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…