easyRNASeq

Count summarization and normalization for RNA-Seq data


Bioconductor version: Release (3.19)

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 "4.4") and enter:


if (!require("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")
geneNetworkR HTML R Script
R / Bioconductor for High Throughput Sequence Analysis PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Genetics, ImmunoOncology, Preprocessing, RNASeq, Software
Version 2.40.1
In Bioconductor since BioC 2.10 (R-2.15) (12.5 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.64.0), BiocFileCache(>= 2.12.0), BiocGenerics(>= 0.50.0), BiocParallel(>= 1.38.0), biomaRt(>= 2.60.1), Biostrings(>= 2.72.1), edgeR(>= 4.2.1), GenomeInfoDb(>= 1.40.1), genomeIntervals(>= 1.60.0), GenomicAlignments(>= 1.40.0), GenomicRanges(>= 1.56.1), SummarizedExperiment(>= 1.34.0), graphics, IRanges(>= 2.38.1), LSD (>= 4.1-0), methods, parallel, rappdirs (>= 0.3.3), Rsamtools(>= 2.20.0), S4Vectors(>= 0.42.1), ShortRead(>= 1.62.0), utils
System Requirements
URL
See More
Suggests BiocStyle(>= 2.32.1), BSgenome(>= 1.72.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.33)
Linking To
Enhances
Depends On Me
Imports Me msgbsR
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package easyRNASeq_2.40.1.tar.gz
Windows Binary easyRNASeq_2.40.1.zip
macOS Binary (x86_64) easyRNASeq_2.40.1.tgz
macOS Binary (arm64) easyRNASeq_2.40.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/easyRNASeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/easyRNASeq
Bioc Package Browser https://code.bioconductor.org/browse/easyRNASeq/
Package Short Url https://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive