easyRNASeq

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data


Bioconductor version: 3.7

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 "3.5") 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")
geneNetworkR HTML R Script
R / Bioconductor for High Throughput Sequence Analysis PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.16.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License Artistic-2.0
Depends
Imports Biobase(>= 2.39.1), BiocGenerics(>= 0.25.1), BiocParallel(>= 1.13.1), biomaRt(>= 2.35.8), Biostrings(>= 2.47.6), DESeq(>= 1.31.0), edgeR(>= 3.21.6), GenomeInfoDb(>= 1.15.2), genomeIntervals(>= 1.35.1), GenomicAlignments(>= 1.15.6), GenomicRanges(>= 1.31.8), SummarizedExperiment(>= 1.9.9), graphics, IRanges(>= 2.13.13), LSD (>= 3.0), locfit, methods, parallel, Rsamtools(>= 1.31.2), S4Vectors(>= 0.17.25), ShortRead(>= 1.37.1), utils
System Requirements
URL
See More
Suggests BiocStyle(>= 2.7.8), BSgenome(>= 1.39.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.31)
Linking To
Enhances
Depends On Me RnaSeqTutorial
Imports Me msgbsR
Suggests Me SeqGSEA
Links To Me
Build Report Build Report

Package Archives

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

Source Package easyRNASeq_2.16.0.tar.gz
Windows Binary easyRNASeq_2.16.0.zip
Mac OS X 10.11 (El Capitan) easyRNASeq_2.16.0.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 https://bioconductor.org/packages/easyRNASeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive