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: 3.2.2
Date: 2015-03-12
Author: Lihua Julie Zhu, Jianhong Ou, 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 <Jianhong.ou@umassmed.edu>
Depends: R (>= 2.10), grid, VennDiagram, biomaRt, IRanges, Biostrings,
        GenomicRanges
Imports: BiocGenerics (>= 0.1.0), GO.db, BSgenome, GenomicFeatures,
        AnnotationDbi, limma, multtest, RBGL, graph, BiocInstaller,
        stats
Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, org.Ce.eg.db,
        org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10,
        BSgenome.Drerio.UCSC.danRer7,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, RUnit, BiocStyle,
        rtracklayer
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
Packaged: 2015-05-19 02:36:50 UTC; biocbuild
NeedsCompilation: no
Built: R 3.2.0; ; 2015-05-19 17:32:55 UTC; unix
