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 (3.1)

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>

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

Installation

To install this package, start R and enter:

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 2.4.0
In Bioconductor since BioC 2.10 (R-2.15) (3 years)
License Artistic-2.0
Depends locfit
Imports Biobase(>= 2.27.1), BiocGenerics(>= 0.13.6), biomaRt(>= 2.23.5), Biostrings(>= 2.35.7), DESeq(>= 1.19.0), edgeR(>= 3.9.11), GenomeInfoDb(>= 1.3.12), genomeIntervals(>= 1.23.0), GenomicAlignments(>= 1.3.27), GenomicRanges(>= 1.19.36), graphics, IRanges(>= 2.1.38), LSD (>= 3.0), methods, parallel, Rsamtools(>= 1.19.27), S4Vectors(>= 0.5.19), ShortRead(>= 1.25.8), utils
LinkingTo
Suggests BiocStyle(>= 1.5.3), BSgenome(>= 1.35.16), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), GenomicFeatures(>= 1.19.18), RnaSeqTutorial(>= 0.3.2), RUnit (>= 0.4.28)
SystemRequirements
Enhances
URL
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me SeqGSEA
Build Report  

Package Archives

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

Package Source easyRNASeq_2.4.0.tar.gz
Windows Binary easyRNASeq_2.4.0.zip
Mac OS X 10.6 (Snow Leopard) easyRNASeq_2.4.0.tgz
Mac OS X 10.9 (Mavericks) easyRNASeq_2.4.0.tgz
Browse/checkout source (username/password: readonly)
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