Package: ChIPpeakAnno
Type: Package
Title: Batch annotation of the peaks identified from either ChIP-seq,
        ChIP-chip experiments or any experiments resulted in large
        number of chromosome ranges
Version: 3.12.7
Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin,
    Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and
    Michael Green
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu>,
 Jianhong Ou <ou.jianhong@gmail.com>
Depends: R (>= 3.2), methods, grid, IRanges (>= 2.11.16), Biostrings,
        GenomicRanges (>= 1.29.14), S4Vectors (>= 0.9.25), VennDiagram
Imports: BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome,
        GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi,
        limma, multtest, RBGL, graph, BiocInstaller, stats, regioneR,
        DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments,
        DelayedArray, SummarizedExperiment, Rsamtools
Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805,
        BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db,
        BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7,
        EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle,
        rtracklayer, knitr, rmarkdown, testthat, trackViewer,
        motifStack, OrganismDbi
Description: The package includes functions to retrieve the sequences
    around the peak, obtain enriched Gene Ontology (GO) terms, find
    the nearest gene, exon, miRNA or custom features such as most
    conserved elements and other transcription factor binding sites
    supplied by users. Starting 2.0.5, new functions have been
    added for finding the peaks with bi-directional promoters with
    summary statistics (peaksNearBDP), for summarizing the
    occurrence of motifs in peaks (summarizePatternInPeaks) and for
    adding other IDs to annotated peaks or enrichedGO (addGeneIDs).
    This package leverages the biomaRt, IRanges, Biostrings,
    BSgenome, GO.db, multtest and stat packages.
License: GPL (>= 2)
LazyLoad: yes
biocViews: Annotation, ChIPSeq, ChIPchip
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2018-02-16 00:43:31 UTC; biocbuild
Built: R 3.4.3; ; 2018-02-16 04:02:10 UTC; windows
