To install this package, start R and enter:

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

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

easyRNASeq

Count summarization and normalization for RNA-Seq data.

Bioconductor version: Release (2.14)

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

Author: Nicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler

Maintainer: Nicolas Delhomme <delhomme at embl.de>

To install this package, start R and enter:

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

Installation

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("easyRNASeq")

 

PDF R Script easyRNASeq
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.0.8
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0
Depends
Imports Biobase(>= 2.24.0), BiocGenerics(>= 0.10.0), biomaRt(>= 2.20.0), Biostrings(>= 2.32.1), DESeq(>= 1.16.0), edgeR(>= 3.6.6), genomeIntervals(>= 1.20.1), GenomicAlignments(>= 1.0.2), GenomicRanges(>= 1.16.3), graphics, IRanges(>= 1.22.9), LSD (>= 2.5), methods, parallel, Rsamtools(>= 1.16.1), ShortRead(>= 1.22.0), utils
Suggests BiocStyle(>= 1.2.0), BSgenome(>= 1.32.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.1000), GenomicFeatures(>= 1.16.2), RnaSeqTutorial(>= 0.2.0), RUnit (>= 0.4.26)
System Requirements
URL
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me SeqGSEA

Package Archives

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

Package Source easyRNASeq_2.0.8.tar.gz
Windows Binary easyRNASeq_2.0.8.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) easyRNASeq_2.0.8.tgz
Mac OS X 10.9 (Mavericks) easyRNASeq_2.0.8.tgz
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