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>

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, ReportWriting, Transcription, GeneExpression, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, 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 2.7.12
Since Bioconductor 2.7 (R-2.12)

Package Downloads

Package Source rnaSeqMap_2.7.12.tar.gz
Windows Binary rnaSeqMap_2.7.12.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary rnaSeqMap_2.7.12.tgz
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