easyRNASeq

DOI: 10.18129/B9.bioc.easyRNASeq    

Count summarization and normalization for RNA-Seq data

Bioconductor version: Release (3.6)

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>

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	2.14.0
In Bioconductor since	BioC 2.10 (R-2.15) (6 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	RnaSeqTutorial
Imports Me	msgbsR
Suggests Me	SeqGSEA
Build Report

Package Archives

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

Source Package	easyRNASeq_2.14.0.tar.gz
Windows Binary	easyRNASeq_2.14.0.zip
Mac OS X 10.11 (El Capitan)	easyRNASeq_2.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/easyRNASeq
Package Short Url	http://bioconductor.org/packages/easyRNASeq/
Package Downloads Report	Download Stats