easyRNASeq

This is the development version of easyRNASeq; for the stable release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

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DOI: 10.18129/B9.bioc.easyRNASeq

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("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")

geneNetworkR HTML R Script

R / Bioconductor for High Throughput Sequence Analysis PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, Genetics, ImmunoOncology, Preprocessing, RNASeq, Software

Version 2.47.0

In Bioconductor since BioC 2.10 (R-2.15) (13.5 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(>= 2.77.2), edgeR(>= 4.2.1), Seqinfo, genomeIntervals(>= 1.60.0), GenomicAlignments(>= 1.45.1), GenomicRanges(>= 1.61.1), SummarizedExperiment(>= 1.39.1), graphics, IRanges(>= 2.38.1), LSD (>= 4.1-0), methods, parallel, rappdirs (>= 0.3.3), Rsamtools(>= 2.25.1), S4Vectors(>= 0.42.1), ShortRead(>= 1.62.0), utils

System Requirements

URL

Suggests BiocStyle(>= 2.32.1), BSgenome(>= 1.72.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.33)

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Package Archives

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

Source Package easyRNASeq_2.47.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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