easyRNASeq

Count summarization and normalization for RNA-Seq data.

Bioconductor version: Development (3.0)

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:

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

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

Documentation

PDF R Script easyRNASeq
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.1.11
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0
Depends
Imports Biobase(>= 2.25.0), BiocGenerics(>= 0.11.3), biomaRt(>= 2.21.1), Biostrings(>= 2.33.12), DESeq(>= 1.17.0), edgeR(>= 3.7.10), genomeIntervals(>= 1.21.1), GenomeInfoDb(>= 1.1.12), GenomicAlignments(>= 1.1.20), GenomicRanges(>= 1.17.23), graphics, IRanges(>= 1.99.21), LSD (>= 2.5), methods, parallel, Rsamtools(>= 1.17.31), S4Vectors(>= 0.1.2), ShortRead(>= 1.23.12), utils
Suggests BiocStyle(>= 1.3.2), BSgenome(>= 1.33.8), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.1000), GenomicFeatures(>= 1.17.12), RnaSeqTutorial(>= 0.3.0), RUnit (>= 0.4.26)
System Requirements
URL
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me SeqGSEA

Package Downloads

Package Source easyRNASeq_2.1.11.tar.gz
Windows Binary easyRNASeq_2.1.11.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) easyRNASeq_2.1.11.tgz
Mac OS X 10.9 (Mavericks) easyRNASeq_2.1.11.tgz
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