easyRNASeq

DOI: 10.18129/B9.bioc.easyRNASeq    

Count summarization and normalization for RNA-Seq data

Bioconductor version: Release (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>

Citation (from within R, enter citation("easyRNASeq")):

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) (8.5 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

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