easyRNASeq

DOI: 10.18129/B9.bioc.easyRNASeq    

Count summarization and normalization for RNA-Seq data

Bioconductor version: Release (3.10)

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 "3.6") 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 2.22.2
In Bioconductor since BioC 2.10 (R-2.15) (7.5 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 easyRNASeq_2.22.2.tar.gz
Windows Binary easyRNASeq_2.22.0.zip
Mac OS X 10.11 (El Capitan) easyRNASeq_2.22.2.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
Old Source Packages for BioC 3.10 Source Archive

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