easyRNASeq

DOI: 10.18129/B9.bioc.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 (3.8)

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("http://bioc.ism.ac.jp/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 R / Bioconductor for High Throughput Sequence Analysis
HTML R Script geneNetworkR
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.17.0
In Bioconductor since BioC 2.10 (R-2.15) (6 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.39.1), BiocGenerics(>= 0.25.1), BiocParallel(>= 1.13.1), biomaRt(>= 2.35.8), Biostrings(>= 2.47.6), DESeq(>= 1.31.0), edgeR(>= 3.21.6), GenomeInfoDb(>= 1.15.2), genomeIntervals(>= 1.35.1), GenomicAlignments(>= 1.15.6), GenomicRanges(>= 1.31.8), SummarizedExperiment(>= 1.9.9), graphics, IRanges(>= 2.13.13), LSD (>= 3.0), locfit, methods, parallel, Rsamtools(>= 1.31.2), S4Vectors(>= 0.17.25), ShortRead(>= 1.37.1), utils
LinkingTo
Suggests BiocStyle(>= 2.7.8), BSgenome(>= 1.39.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.31)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me msgbsR
Suggests Me SeqGSEA
Build Report  

Package Archives

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

Source Package easyRNASeq_2.17.0.tar.gz
Windows Binary easyRNASeq_2.17.0.zip
Mac OS X 10.11 (El Capitan) easyRNASeq_2.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/easyRNASeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/easyRNASeq
Package Short Url http://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats

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