easyRNASeq

DOI: 10.18129/B9.bioc.easyRNASeq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: 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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("easyRNASeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("easyRNASeq")

 

HTML	R Script	geneNetworkR
PDF	R Script	R / Bioconductor for High Throughput Sequence Analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Genetics, ImmunoOncology, Preprocessing, RNASeq, Software
Version	2.18.4
In Bioconductor since	BioC 2.10 (R-2.15) (7 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
Links To Me
Build Report

Package Archives

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

Source Package	easyRNASeq_2.18.4.tar.gz
Windows Binary	easyRNASeq_2.18.3.zip
Mac OS X 10.11 (El Capitan)	easyRNASeq_2.18.4.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