compcodeR

DOI: 10.18129/B9.bioc.compcodeR    

This package is for version 3.8 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: 3.8

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

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Installation

To install this package, start R (version "3.5") 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	1.18.1
In Bioconductor since	BioC 2.14 (R-3.1) (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_1.18.1.tar.gz
Windows Binary	compcodeR_1.18.1.zip
Mac OS X 10.11 (El Capitan)	compcodeR_1.18.1.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	http://bioconductor.org/packages/compcodeR/
Package Downloads Report	Download Stats