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Showing content from https://www.bioconductor.org/packages/release/bioc/html/easyRNASeq.html below:

Bioconductor - easyRNASeq

easyRNASeq

This is the released version of easyRNASeq; for the devel version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: Release (3.21)

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 "4.5") 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")

Details biocViews GeneExpression, Genetics, ImmunoOncology, Preprocessing, RNASeq, Software Version 2.44.0 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(>= 2.72.1), 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 Package Archives

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

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