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compcodeR

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DifferentialExpression, ImmunoOncology, RNASeq, Software
Version 1.38.0
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
System Requirements
URL https://github.com/csoneson/compcodeR
Bug Reports https://github.com/csoneson/compcodeR/issues
See More
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

Package Archives

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

Source Package compcodeR_1.38.0.tar.gz
Windows Binary compcodeR_1.38.0.zip
macOS Binary (x86_64) compcodeR_1.38.0.tgz
macOS Binary (arm64) compcodeR_1.38.0.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