Package: Repitools
Version: 1.20.0
Date: 2016/10/07
Title: Epigenomic tools
Author: Mark Robinson <mark.robinson@imls.uzh.ch>, Dario Strbenac
        <dario.strbenac@sydney.edu.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: parallel, S4Vectors (>= 0.9.25), IRanges (>= 1.20.0),
        GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
        GenomicAlignments, rtracklayer, BSgenome, gplots, grid, MASS,
        gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix,
        Rsolnp, cluster
Suggests: 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,
        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
        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: 2016-10-17 22:48:01 UTC; biocbuild
biocViews: DNAMethylation, GeneExpression, MethylSeq
NeedsCompilation: yes
Built: R 3.4.1; x86_64-pc-linux-gnu; 2017-09-24 17:23:46 UTC; unix
