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

Bioconductor version: Release (3.19)

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]

Maintainer: Charlotte Soneson <charlottesoneson at>

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


To install this package, start R (version "4.4") 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:

compcodeR HTML R Script
phylocompcodeR HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, ImmunoOncology, RNASeq, Software
Version 1.40.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL (>= 2)
Depends R (>= 4.0), sm
Imports 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, rmarkdown, shiny, shinydashboard
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Suggests BiocStyle, EBSeq, DESeq2(>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk
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Follow Installation instructions to use this package in your R session.

Source Package compcodeR_1.40.0.tar.gz
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macOS Binary (x86_64) compcodeR_1.40.0.tgz
macOS Binary (arm64) compcodeR_1.40.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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