To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("compcodeR")

In most cases, you don't need to download the package archive at all.

compcodeR

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

Bioconductor version: Release (2.14)

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 <Charlotte.Soneson at isb-sib.ch>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("compcodeR")

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, RNASeq, Software
Version 1.0.0
In Bioconductor since BioC 2.14 (R-3.1)
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
Suggests BiocStyle, EBSeq, DESeq, DESeq2(>= 1.1.31), baySeq(>= 1.16.0), genefilter, NOISeq, DSS, TCC, samr, NBPSeq, HTSDiff
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source compcodeR_1.0.0.tar.gz
Windows Binary compcodeR_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) compcodeR_1.0.0.tgz
Mac OS X 10.9 (Mavericks) compcodeR_1.0.0.tgz
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