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 (3.13)

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 "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.27.1
In Bioconductor since BioC 2.10 (R-2.15) (8.5 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.50.0), BiocFileCache(>= 1.14.0), BiocGenerics(>= 0.36.0), BiocParallel(>= 1.24.1), biomaRt(>= 2.46.0), Biostrings(>= 2.58.0), edgeR(>= 3.32.0), GenomeInfoDb(>= 1.26.0), genomeIntervals(>= 1.46.0), GenomicAlignments(>= 1.26.0), GenomicRanges(>= 1.42.0), SummarizedExperiment(>= 1.20.0), graphics, IRanges(>= 2.24.0), LSD (>= 4.1-0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools(>= 2.6.0), S4Vectors(>= 0.28.0), ShortRead(>= 1.48.0), utils
LinkingTo
Suggests BiocStyle(>= 2.18.0), BSgenome(>= 1.58.0), 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 easyRNASeq_2.27.1.tar.gz
Windows Binary easyRNASeq_2.27.1.zip
macOS 10.13 (High Sierra) easyRNASeq_2.27.1.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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