rnaSeqMap

rnaSeq secondary analyses

Bioconductor version: 2.10

Provides means of analysis for RNAseq data, used together with genomic annotation. 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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("rnaSeqMap")

To cite this package in a publication, start R and enter:

    citation("rnaSeqMap")

Documentation

PDF	R Script	rnaSeqMap primer
PDF		Reference Manual

Details

biocViews	Annotation, Bioinformatics, DifferentialExpression, GeneExpression, HighThroughputSequencing, RNAseq, ReportWriting, SAGE, Software, Transcription, Visualization
Depends	R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools
Imports	GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0)
Suggests
System Requirements
License	GPL-2
URL
Depends On Me
Imports Me
Suggests Me
Version	2.10.0
Since	Bioconductor 2.7 (R-2.12)

Package Downloads

Package Source	rnaSeqMap_2.10.0.tar.gz
Windows Binary
MacOS 10.5 (Leopard) binary	rnaSeqMap_2.10.0.tgz
Package Downloads Report	Download Stats

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