easyRNASeq

DOI: 10.18129/B9.bioc.easyRNASeq    

Count summarization and normalization for RNA-Seq data

Bioconductor version: Release (3.9)

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 2.20.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License Artistic-2.0
Depends
Imports Biobase(>= 2.41.2), BiocFileCache(>= 1.7.10), BiocGenerics(>= 0.27.1), BiocParallel(>= 1.15.15), biomaRt(>= 2.37.9), Biostrings(>= 2.49.2), DESeq(>= 1.33.0), edgeR(>= 3.23.6), GenomeInfoDb(>= 1.17.4), genomeIntervals(>= 1.37.0), GenomicAlignments(>= 1.17.3), GenomicRanges(>= 1.33.14), SummarizedExperiment(>= 1.11.6), graphics, IRanges(>= 2.15.18), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools(>= 1.33.7), S4Vectors(>= 0.19.23), ShortRead(>= 1.39.0), utils
LinkingTo
Suggests BiocStyle(>= 2.9.6), BSgenome(>= 1.49.5), 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_2.20.0.tar.gz
Windows Binary easyRNASeq_2.20.0.zip
Mac OS X 10.11 (El Capitan) easyRNASeq_2.20.0.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 http://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats

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