easyRNASeq

Count summarization and normalization for RNA-Seq data.

Bioconductor version: Release (2.12)

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

Maintainer: Nicolas Delhomme <delhomme at embl.de>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("easyRNASeq")

Documentation

PDF	R Script	RNA-Seq
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Genetics, Preprocessing, RNAseq, Software
Version	1.6.4
In Bioconductor since	BioC 2.10 (R-2.15)
License	Artistic-2.0
Depends	graphics, methods, parallel, utils, genomeIntervals(>= 1.16.0), Biobase(>= 2.20.1), BiocGenerics(>= 0.6.0), biomaRt(>= 2.16.0), edgeR(>= 3.2.4), Biostrings(>= 2.28.0), BSgenome(>= 1.28.0), DESeq(>= 1.12.1), GenomicRanges(>= 1.12.5), IRanges(>= 1.18.4), LSD (>= 2.5), Rsamtools(>= 1.12.4), ShortRead(>= 1.18.0)
Imports
Suggests	BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.17), GenomicFeatures(>= 1.11.0), RnaSeqTutorial(>= 0.0.11)
System Requirements
URL
Depends On Me	RnaSeqTutorial
Imports Me
Suggests Me

Package Downloads

Package Source	easyRNASeq_1.6.4.tar.gz
Windows Binary	easyRNASeq_1.6.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	easyRNASeq_1.6.4.tgz
Package Downloads Report	Download Stats

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