easyRNASeq

DOI: 10.18129/B9.bioc.easyRNASeq    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: 3.12

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 "4.0") 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

PDF		Reference Manual

Details

biocViews	GeneExpression, Genetics, ImmunoOncology, Preprocessing, RNASeq, Software
Version	2.26.0
In Bioconductor since	BioC 2.10 (R-2.15) (9 years)
License	Artistic-2.0
Depends
Imports	Biobase(>= 2.44.0), BiocFileCache(>= 1.7.10), BiocGenerics(>= 0.30.0), BiocParallel(>= 1.18.1), biomaRt(>= 2.40.5), Biostrings(>= 2.52.0), DESeq(>= 1.36.0), edgeR(>= 3.26.8), GenomeInfoDb(>= 1.20.0), genomeIntervals(>= 1.40.0), GenomicAlignments(>= 1.20.1), GenomicRanges(>= 1.36.1), SummarizedExperiment(>= 1.14.1), graphics, IRanges(>= 2.18.3), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools(>= 2.0.3), S4Vectors(>= 0.22.1), ShortRead(>= 1.42.0), utils
LinkingTo
Suggests	BiocStyle(>= 2.12.0), BSgenome(>= 1.52.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32)
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
Windows Binary
macOS 10.13 (High Sierra)	easyRNASeq_2.26.0.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	https://bioconductor.org/packages/easyRNASeq/
Package Downloads Report	Download Stats