Package: rnaSeqMap
Type: Package
Title: rnaSeq secondary analyses
Version: 2.10.0
Date: 2011-10-24
Author: Anna Lesniewska <alesniewska@cs.put.poznan.pl>; Michal Okoniewski <michal@fgcz.ethz.ch>
Maintainer: Michal Okoniewski <michal@fgcz.ethz.ch>
Depends: R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools
Imports: GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0)
Suggests:
Description: 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. 
License: GPL-2
URL:
biocViews: Annotation, Bioinformatics, ReportWriting, Transcription,
        GeneExpression, DifferentialExpression,
        HighThroughputSequencing, RNAseq, SAGE, Visualization
Collate: zzz.R utils.R plots.R NucleotideDistr.R SeqReads.R NDplots.R
        NDtransforms.R bam2sig.R parseGff3.R pipelines.R
        normalizations.R measures.R generators.R
Packaged: 2012-03-31 06:28:08 UTC; biocbuild
