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: 3.4.6
Date: 2016-02-10
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 <Jianhong.ou@umassmed.edu>
Depends: R (>= 3.1), methods, grid, IRanges, Biostrings, GenomicRanges,
        S4Vectors, VennDiagram
Imports: BiocGenerics (>= 0.15.1), GO.db, biomaRt, BSgenome,
        GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi,
        limma, multtest, RBGL, graph, BiocInstaller, stats, regioneR,
        DBI, ensembldb, Biobase
Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, 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, RUnit, BiocStyle,
        rtracklayer, knitr
Description: The package is to facilitate the downstream analysis for 
        ChIP-seq experiments. It includes functions to find  the nearest 
        gene, exon, miRNA or custom features such as the most conserved 
        elements and other transcription factor binding sites supplied 
        by users, retrieve the sequences around the peak, obtain enriched 
        Gene Ontology (GO) terms or pathways. 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). Starting 3.4, we also 
        implement functions for permutation test to determine the association 
        between two sets of peaks, and to plot heatmaps for given feature/peak 
        ranges. 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
NeedsCompilation: no
Packaged: 2016-02-12 02:06:54 UTC; biocbuild
Built: R 3.2.3; ; 2016-10-26 18:00:28 UTC; unix