To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rnaSeqMap")

In most cases, you don't need to download the package archive at all.

rnaSeqMap

   

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see rnaSeqMap.

rnaSeq analyses using xmapcore database

Bioconductor version: 2.8

Provides means of analysis for RNAseq data, used together with genomic annotation from Ensembl. Requires a set of BAM files on the input or alternatively, an xmapcore database in MySQL as a back-end, which is also a storage for sequencing reads. Front-end analyses include transformations of the coverage function, splicing analysis, finding irreducible regions with the two-sliding-windows algorithm and genomic region visualizations.

Author: Anna Lesniewska <alesniewska at cs.put.poznan.pl>; Michal Okoniewski <michal at fgcz.ethz.ch>

Maintainer: Michal Okoniewski <michal at fgcz.ethz.ch>

Citation (from within R, enter citation("rnaSeqMap")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rnaSeqMap")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rnaSeqMap")

 

PDF rnaSeqMap.pdf
PDF   Reference Manual

Details

biocViews Annotation, Bioinformatics, DifferentialExpression, GeneExpression, HighThroughputSequencing, RNAseq, ReportWriting, SAGE, Software, Transcription, Visualization
Version 2.7.12
In Bioconductor since BioC 2.7 (R-2.12) (5.5 years)
License GPL-2
Depends R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools
Imports GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0)
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source rnaSeqMap_2.7.12.tar.gz
Windows Binary rnaSeqMap_2.7.12.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/rnaSeqMap/tree/release-2.8
Package Short Url http://bioconductor.org/packages/rnaSeqMap/
Package Downloads Report Download Stats

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