easyRNASeq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.
Count summarization and normalization for RNA-Seq data
Bioconductor version: 3.9
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 "3.6") 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, ImmunoOncology, Preprocessing, RNASeq, Software |
| Version | 2.20.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | Biobase(>= 2.41.2), BiocFileCache(>= 1.7.10), BiocGenerics(>= 0.27.1), BiocParallel(>= 1.15.15), biomaRt(>= 2.37.9), Biostrings(>= 2.49.2), DESeq(>= 1.33.0), edgeR(>= 3.23.6), GenomeInfoDb(>= 1.17.4), genomeIntervals(>= 1.37.0), GenomicAlignments(>= 1.17.3), GenomicRanges(>= 1.33.14), SummarizedExperiment(>= 1.11.6), graphics, IRanges(>= 2.15.18), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools(>= 1.33.7), S4Vectors(>= 0.19.23), ShortRead(>= 1.39.0), utils |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle(>= 2.9.6), BSgenome(>= 1.49.5), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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_2.20.0.tar.gz |
| Windows Binary | easyRNASeq_2.20.0.zip |
| Mac OS X 10.11 (El Capitan) | easyRNASeq_2.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/easyRNASeq |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |