compcodeR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

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

Bioconductor version: Release (3.23)

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

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

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

Charlotte Soneson, Paul Bastide, Mélina Gallopin. compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods. doi:10.18129/B9.bioc.compcodeR, R package version 1.48.1, https://bioconductor.org/packages/compcodeR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, ImmunoOncology, RNASeq, Software
Version	1.48.1
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 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, statip, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard
System Requirements
URL	https://github.com/csoneson/compcodeR
Bug Reports	https://github.com/csoneson/compcodeR/issues

Suggests	BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk
Linking To
Enhances	rpanel, DSS
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	compcodeR_1.48.1.tar.gz
Windows Binary (x86_64)	compcodeR_1.48.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	compcodeR_1.48.1.tgz
macOS Binary (sonoma-arm64)	compcodeR_1.48.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/compcodeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/compcodeR
Package Short Url	https://bioconductor.org/packages/compcodeR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive