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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("easyRNASeq")
In most cases, you don't need to download the package archive at all.
easyRNASeq
|
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.
Count summarization and normalization for RNA-Seq data.
Bioconductor version: 2.12
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
Maintainer: Nicolas Delhomme <delhomme at embl.de>
Citation (from within R,
enter citation("easyRNASeq")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("easyRNASeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("easyRNASeq")
| R Script | RNA-Seq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, Genetics, Preprocessing, RNAseq, Software |
| Version | 1.6.4 |
| In Bioconductor since | BioC 2.10 (R-2.15) (4 years) |
| License | Artistic-2.0 |
| Depends | graphics, methods, parallel, utils, genomeIntervals(>= 1.16.0), Biobase(>= 2.20.1), BiocGenerics(>= 0.6.0), biomaRt(>= 2.16.0), edgeR(>= 3.2.4), Biostrings(>= 2.28.0), BSgenome(>= 1.28.0), DESeq(>= 1.12.1), GenomicRanges(>= 1.12.5), IRanges(>= 1.18.4), LSD (>= 2.5), Rsamtools(>= 1.12.4), ShortRead(>= 1.18.0) |
| Imports | |
| LinkingTo | |
| Suggests | BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.17), GenomicFeatures(>= 1.11.0), RnaSeqTutorial(>= 0.0.11) |
| SystemRequirements | |
| Enhances | edgeR, genomeIntervals, DESeq, ShortRead |
| URL | |
| Depends On Me | RnaSeqTutorial |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | easyRNASeq_1.6.4.tar.gz |
| Windows Binary | easyRNASeq_1.6.4.zip |
| Mac OS X 10.6 (Snow Leopard) | easyRNASeq_1.6.4.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/easyRNASeq/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/easyRNASeq/ |
| Package Downloads Report | Download Stats |
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