Package: Repitools
Version: 1.8.6
Date: 2013/12/12
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, 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)
biocViews: DNAMethylation, GeneExpression, Methylseq
Packaged: 2013-12-12 08:48:37 UTC; biocbuild
Built: R 3.0.2; i386-w64-mingw32; 2013-12-12 16:55:31 UTC; windows
Archs: i386, x64
