To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("easyRNASeq")

In most cases, you don't need to download the package archive at all.

easyRNASeq

   

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: 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:

## try http:// if https:// URLs are not supported
source("https://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 2.4.7
In Bioconductor since BioC 2.10 (R-2.15) (4 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.28.0), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.7), biomaRt(>= 2.24.0), Biostrings(>= 2.36.1), DESeq(>= 1.20.0), edgeR(>= 3.10.2), genomeIntervals(>= 1.24.1), GenomicAlignments(>= 1.4.1), GenomeInfoDb(>= 1.4.1), GenomicRanges(>= 1.20.5), graphics, IRanges(>= 2.2.5), LSD (>= 3.0), methods, parallel, Rsamtools(>= 1.20.4), S4Vectors(>= 0.6.1), ShortRead(>= 1.26.0), locfit, utils
LinkingTo
Suggests BiocStyle(>= 1.6.0), BSgenome(>= 1.36.2), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), GenomicFeatures(>= 1.20.1), RnaSeqTutorial(>= 0.6.0), 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_2.4.7.tar.gz
Windows Binary easyRNASeq_2.4.7.zip
Mac OS X 10.6 (Snow Leopard) easyRNASeq_2.4.7.tgz
Mac OS X 10.9 (Mavericks) easyRNASeq_2.4.7.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/easyRNASeq/tree/release-3.1
Package Short Url http://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats

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