Package: Repitools
Version: 1.44.0
Date: 2021-11-21
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 (>= 3.5.0), methods, BiocGenerics (>= 0.8.0)
Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
        GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
        GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots,
        grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo, 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: 2022-11-01 22:43:15 UTC; biocbuild
biocViews: DNAMethylation, GeneExpression, MethylSeq
git_url: https://git.bioconductor.org/packages/Repitools
git_branch: RELEASE_3_16
git_last_commit: 5f359d2
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: yes
Built: R 4.2.2; x86_64-conda-linux-gnu; 2022-11-09 09:50:15 UTC; unix
