DOI: 10.18129/B9.bioc.compcodeR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see compcodeR.

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

Bioconductor version: 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>

Citation (from within R, enter citation("compcodeR")):


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

if (!require("BiocManager", quietly = TRUE))


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


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



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


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
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
Enhances rpanel, DSS
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
macOS Binary (x86_64) compcodeR_1.34.0.tgz
macOS Binary (arm64) compcodeR_1.34.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: