Package: Repitools
Version: 1.2.0
Date: 2012/3/14
Title: Epigenomic tools
Author: Mark Robinson <mark.robinson@imls.uzh.ch>, Dario Strbenac <d.strbenac@garvan.org.au>, Aaron Statham <a.statham@garvan.org.au>
Maintainer: Mark Robinson <mark.robinson@imls.uzh.ch>
LazyLoad: Yes
Depends: R (>= 2.13.0), methods, BiocGenerics (>= 0.1.0), GenomicRanges
        (>= 1.7.8)
Imports: BiocGenerics, IRanges (>= 1.13.5), GenomicRanges, BSgenome,
        gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo,
        aroma.affymetrix
Suggests: GenomicRanges, IRanges, BSgenome, gplots, grid, MASS,
        gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead,
        BSgenome.Hsapiens.UCSC.hg18
Description: Tools for the analysis of enrichment-based epigenomic data.  Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, etc. 
Collate: classes.R multiHeatmap.R BAM2GRanges.R FastQC-class.R
        plotClusters.R annoDF2GR.R GCbiasPlots.R featureScores.R
        profilePlots.R findClusters.R mergeReplicates.R
        processNimblegenArrays.R regionStats.R cpgDensityPlot.R
        featureBlocks.R getProbePositionsDf.R genomeBlocks.R
        mappabilityCalc.R ChromaBlocks.R writeWig.R makeWindowLookup.R
        sequenceCalc.R genQC.R annoGR2DF.R gcContentCalc.R
        GCadjustCopy.R enrichmentPlot.R cpgBoxplots.R GDL2GRL.R utils.R
        absoluteCN.R annotationLookup.R cpgDensityCalc.R blocksStats.R
        binPlots.R chromosomeCNplots.R checkProbes.R relativeCN.R
        enrichmentCalc.R clusterPlots.R summarizeScores.R
License: LGPL (>= 2)
biocViews: DNAmethylation, GeneExpression, Methylseq
Packaged: 2012-03-31 09:02:38 UTC; biocbuild
Built: R 2.15.0; ; 2012-03-31 12:50:00 UTC; windows
