compcodeR

DOI: 10.18129/B9.bioc.compcodeR  

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Bioconductor version: Release (3.16)

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

Author: Charlotte Soneson [aut, cre] , Paul Bastide [aut] , Mélina Gallopin [aut] (0000-0002-2431-7825 )

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("compcodeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("compcodeR")

 

HTML	R Script	compcodeR
HTML	R Script	phylocompcodeR
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, Software
Version	1.34.0
In Bioconductor since	BioC 2.14 (R-3.1) (9 years)
License	GPL (>= 2)
Depends	R (>= 4.0), sm
Imports	tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics
LinkingTo
Suggests	BiocStyle, EBSeq, DESeq2(>= 1.1.31), baySeq(>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown, phytools, phangorn, testthat, ggtree, tidytree, statmod, covr
SystemRequirements
Enhances	rpanel, DSS
URL	https://github.com/csoneson/compcodeR
BugReports	https://github.com/csoneson/compcodeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	compcodeR_1.34.0.tar.gz
Windows Binary	compcodeR_1.34.0.zip
macOS Binary (x86_64)	compcodeR_1.34.0.tgz
macOS Binary (arm64)	compcodeR_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/compcodeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/compcodeR
Bioc Package Browser	https://code.bioconductor.org/browse/compcodeR/
Package Short Url	https://bioconductor.org/packages/compcodeR/
Package Downloads Report	Download Stats