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compcodeR

This is the released version of compcodeR; for the devel version, see compcodeR.

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


Bioconductor version: Release (3.21)

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] ORCID iD ORCID: 0000-0003-3833-2169 , Paul Bastide [aut] ORCID iD ORCID: 0000-0002-8084-9893 , Mélina Gallopin [aut] ORCID iD ORCID: 0000-0002-2431-7825

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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")
compcodeRHTMLR Script
phylocompcodeRHTMLR Script
Reference ManualPDF
NEWSText

Details

biocViewsDifferentialExpression, ImmunoOncology, RNASeq, Software
Version1.44.0
In Bioconductor sinceBioC 2.14 (R-3.1) (11 years)
LicenseGPL (>= 2)
DependsR (>= 4.0), sm
Importsknitr (>= 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
System Requirements
URLhttps://github.com/csoneson/compcodeR
Bug Reportshttps://github.com/csoneson/compcodeR/issues
See More
SuggestsBiocStyle, EBSeq, DESeq2(>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk
Linking To
Enhancesrpanel, DSS
Depends On Me
Imports Me
Suggests Me
Links To Me
Build ReportBuild Report

Package Archives

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

Source PackagecompcodeR_1.44.0.tar.gz
Windows Binary (x86_64) compcodeR_1.44.0.zip (64-bit only)
macOS Binary (x86_64)compcodeR_1.44.0.tgz
macOS Binary (arm64)compcodeR_1.44.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/compcodeR
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/compcodeR
Bioc Package Browserhttps://code.bioconductor.org/browse/compcodeR/
Package Short Urlhttps://bioconductor.org/packages/compcodeR/
Package Downloads ReportDownload Stats
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