rnaSeqMap

rnaSeq analyses using xmapcore database

Bioconductor version: Development (2.8)

Provides means of analysis for RNAseq data, used together with genomic annotation from Ensembl. Requires 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 ; Michal Okoniewski

Maintainer: Michal Okoniewski

To install this package, start R and enter:

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

Documentation

PDF

R Script

rnaSeqMap primer

Reference Manual

Details

biocViews	Annotation, Bioinformatics, ReportWriting, Transcription, GeneExpression, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Visualization
Depends	R, methods, xmapcore
Imports	Biobase, IRanges, edgeR, DESeq, DBI, RMySQL
Suggests
System Requirements
License	GPL-2
URL
Depends On Me
Imports Me
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Version	1.1.0

Package Downloads

Package Source	rnaSeqMap_1.1.0.tar.gz
Windows Binary	rnaSeqMap_1.1.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	rnaSeqMap_1.1.0.tgz
Package Downloads Report	Download Stats