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

 

Count summarization and normalization for RNA-Seq data

Bioconductor version: Release (3.2)

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, Niklas Maehler

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
HTML R Script A walkthrough the easyRNASeq package functionalities
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.6.1
In Bioconductor since BioC 2.10 (R-2.15) (4 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.30.0), BiocGenerics(>= 0.16.1), BiocParallel(>= 1.4.0), biomaRt(>= 2.26.1), Biostrings(>= 2.38.2), DESeq(>= 1.22.0), edgeR(>= 3.12.0), GenomeInfoDb(>= 1.6.1), genomeIntervals(>= 1.26.0), GenomicAlignments(>= 1.6.1), GenomicRanges(>= 1.22.1), SummarizedExperiment(>= 1.0.1), graphics, IRanges(>= 2.4.4), LSD (>= 3.0), locfit, methods, parallel, Rsamtools(>= 1.22.0), S4Vectors(>= 0.8.3), ShortRead(>= 1.28.0), utils
LinkingTo
Suggests BiocStyle(>= 1.8.0), BSgenome(>= 1.38.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, GenomicFeatures(>= 1.22.5), knitr, rmarkdown, RnaSeqTutorial(>= 0.7.0), RUnit (>= 0.4.31)
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_2.6.1.tar.gz
Windows Binary easyRNASeq_2.6.1.zip
Mac OS X 10.6 (Snow Leopard) easyRNASeq_2.6.0.tgz
Mac OS X 10.9 (Mavericks) easyRNASeq_2.6.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/easyRNASeq/tree/release-3.2
Package Short Url http://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats

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