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 is the development version of easyRNASeq; for the stable release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: Development (3.4)

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 <nicolas.delhomme at umu.se>

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 geneNetworkR
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.9.2
In Bioconductor since BioC 2.10 (R-2.15) (4 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.31.3), BiocGenerics(>= 0.17.2), BiocParallel(>= 1.5.1), biomaRt(>= 2.27.2), Biostrings(>= 2.39.3), DESeq(>= 1.23.0), edgeR(>= 3.13.4), GenomeInfoDb(>= 1.7.3), genomeIntervals(>= 1.27.0), GenomicAlignments(>= 1.7.3), GenomicRanges(>= 1.23.16), SummarizedExperiment(>= 1.1.11), graphics, IRanges(>= 2.5.27), LSD (>= 3.0), locfit, methods, parallel, Rsamtools(>= 1.23.1), S4Vectors(>= 0.9.38), ShortRead(>= 1.29.1), utils
LinkingTo
Suggests BiocStyle(>= 1.9.2), BSgenome(>= 1.39.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, GenomicFeatures(>= 1.23.15), knitr, rmarkdown, RnaSeqTutorial (>= 0.9.0), RUnit (>= 0.4.31)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me SeqGSEA
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source easyRNASeq_2.9.2.tar.gz
Windows Binary easyRNASeq_2.9.2.zip
Mac OS X 10.9 (Mavericks) easyRNASeq_2.9.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/easyRNASeq
Package Short Url http://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats

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