Package: ChIPpeakAnno
Type: Package
Title: Batch annotation of the peaks identified from either ChIP-seq,
        ChIP-chip experiments, or any experiments that result in large
        number of genomic interval data
Version: 3.44.0
Encoding: UTF-8
Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui
        Li, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson,
        Simon Lin, David Lapointe, Michael Green
Maintainer: Jianhong Ou <jou@morgridge.org>, Lihua Julie Zhu
 <julie.zhu@umassmed.edu>, Kai Hu <kai.hu@umassmed.edu>, Junhui
 Li <junhui.li@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), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments,
        GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment,
        VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics,
        grid, InteractionSet, KEGGREST, matrixStats, multtest,
        regioneR, rtracklayer, stats, utils, universalmotif, stringr,
        tibble, tidyr, data.table, scales, ensembldb
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, EnsDb.Hsapiens.v86,
        TxDb.Hsapiens.UCSC.hg18.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR,
        knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack,
        OrganismDbi, BiocFileCache
Description: The package encompasses a range of functions for
        identifying the closest gene, exon, miRNA, or custom
        features—such as highly conserved elements and user-supplied
        transcription factor binding sites. Additionally, users can
        retrieve sequences around the peaks and obtain enriched Gene
        Ontology (GO) or Pathway terms. In version 2.0.5 and beyond,
        new functionalities have been introduced. These include
        features for identifying peaks associated with bi-directional
        promoters along with summary statistics (peaksNearBDP),
        summarizing motif occurrences in peaks
        (summarizePatternInPeaks), and associating additional
        identifiers with annotated peaks or enrichedGO (addGeneIDs).
        The package integrates with various other packages such as
        biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and
        stat to enhance its analytical capabilities.
License: GPL (>= 2)
LazyLoad: yes
LazyData: true
LazyDataCompression: xz
biocViews: Annotation, ChIPSeq, ChIPchip
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:03:18 UTC
RemoteUrl: https://github.com/bioc/ChIPpeakAnno
RemoteRef: RELEASE_3_22
RemoteSha: 2b855fafe98cd49218850fdb4d5f11c7d91e5a05
NeedsCompilation: no
Packaged: 2025-11-11 16:04:26 UTC; root
Built: R 4.5.2; ; 2025-11-11 16:25:37 UTC; windows
