easyRNASeq

Count summarization and normalization for RNA-Seq data.

Bioconductor version: 2.10

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
Depends	graphics, methods, parallel, utils, genomeIntervals(>= 1.12.0), Biobase(>= 2.16.0), BiocGenerics(>= 0.2.0), biomaRt(>= 2.12.0), edgeR(>= 2.6.10), Biostrings(>= 2.24.1), BSgenome(>= 1.24.0), DESeq(>= 1.8.3), GenomicRanges(>= 1.8.12), IRanges(>= 1.14.4), Rsamtools(>= 1.8.6), ShortRead(>= 1.14.4)
Imports
Suggests	BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.17), GenomicFeatures(>= 1.8.2), RnaSeqTutorial(>= 0.0.8)
System Requirements
License	Artistic-2.0
URL
Depends On Me	RnaSeqTutorial
Imports Me
Suggests Me
Version	1.2.5
Since	Bioconductor 2.10 (R-2.15)

Package Downloads

Package Source	easyRNASeq_1.2.5.tar.gz
Windows Binary	easyRNASeq_1.2.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	easyRNASeq_1.2.5.tgz
Package Downloads Report	Download Stats

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