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

easyRNASeq

Count summarization and normalization for RNA-Seq data.

Bioconductor version: 2.13

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>

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	1.8.8
In Bioconductor since	BioC 2.10 (R-2.15)
License	Artistic-2.0
Depends	genomeIntervals(>= 1.18.0), Biobase(>= 2.22.0), biomaRt(>= 2.18.0), edgeR(>= 3.4.0), Biostrings(>= 2.30.0), DESeq(>= 1.14.0), GenomicRanges(>= 1.14.3), IRanges(>= 1.20.5), Rsamtools(>= 1.14.1), ShortRead(>= 1.20.0)
Imports	graphics, methods, parallel, utils, BiocGenerics(>= 0.8.0), LSD (>= 2.5)
Suggests	BSgenome(>= 1.30.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.19), GenomicFeatures(>= 1.14.0), RnaSeqTutorial(>= 0.0.13), BiocStyle(>= 1.0.0)
System Requirements
URL
Depends On Me	RnaSeqTutorial
Imports Me
Suggests Me

Package Archives

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

Package Source	easyRNASeq_1.8.8.tar.gz
Windows Binary	easyRNASeq_1.8.8.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	easyRNASeq_1.8.8.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats