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: 3.34.1
Encoding: UTF-8
Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, 
    Hervé Pagès, Claude Gazin,
    Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and
    Michael Green
Maintainer: Jianhong Ou <jianhong.ou@duke.edu>,
 Lihua Julie Zhu <julie.zhu@umassmed.edu>
Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>=
        1.31.8), S4Vectors (>= 0.17.25)
Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>=
        2.47.6), DBI, dplyr, ensembldb, GenomeInfoDb,
        GenomicAlignments, GenomicFeatures, RBGL, Rsamtools,
        SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices,
        graph, graphics, grid, InteractionSet, KEGGREST, matrixStats,
        multtest, regioneR, rtracklayer, stats, utils
Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager,
        BiocStyle, BSgenome.Ecoli.NCBI.20080805,
        BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db,
        BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7,
        BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr,
        EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR,
        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
LazyData: true
LazyDataCompression: xz
biocViews: Annotation, ChIPSeq, ChIPchip
VignetteBuilder: knitr
RoxygenNote: 7.2.3
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: RELEASE_3_17
git_last_commit: 1a47186
git_last_commit_date: 2023-04-26
Date/Publication: 2023-04-27
NeedsCompilation: no
Packaged: 2023-04-27 20:24:15 UTC; biocbuild
Built: R 4.3.1; ; 2023-08-30 20:04:12 UTC; unix
