Package: Repitools
Version: 1.10.1
Date: 2014/03/20
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>, Andrea Riebler
        <andrea.riebler@math.ntnu.no>
Maintainer: Mark Robinson <mark.robinson@imls.uzh.ch>
LazyLoad: Yes
Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0)
Imports: IRanges (>= 1.20.0), GenomicRanges, GenomicAlignments,
        BSgenome, gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0),
        DNAcopy, Ringo, aroma.affymetrix, Rsolnp, parallel, Biostrings,
        Rsamtools, cluster
Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18, rtracklayer
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,
        BayMeth for quantifying methylation 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 abcdDNA.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 determineOffset.R empBayes.R methylEst.R
        hyper.R maskOut.R
License: LGPL (>= 2)
Packaged: 2014-04-16 10:44:22 UTC; biocbuild
biocViews: DNAMethylation, GeneExpression, MethylSeq
Built: R 3.1.0; i386-w64-mingw32; 2014-04-16 17:17:17 UTC; windows
Archs: i386, x64
