compcodeR

DOI: 10.18129/B9.bioc.compcodeR    

This package is for version 3.9 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: 3.9

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 and interfaces to several packages for performing the differential expression analysis.

Author: Charlotte Soneson [aut, cre]

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF R Script compcodeR
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, ImmunoOncology, RNASeq, Software
Version 1.20.1
In Bioconductor since BioC 2.14 (R-3.1) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.0.2), sm
Imports tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, gdata, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods
LinkingTo
Suggests BiocStyle, EBSeq, DESeq, DESeq2(>= 1.1.31), baySeq(>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0)
SystemRequirements
Enhances rpanel, DSS
URL
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_1.20.1.tar.gz
Windows Binary compcodeR_1.20.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) compcodeR_1.20.1.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

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