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("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 | R Script | |
Reference Manual | ||
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 |