ChIPpeakAnno : Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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: 3.6.4
Date: 2016-05-11
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 (>= 3.2), methods, grid, IRanges (>= 2.5.27), Biostrings,
GenomicRanges (>= 1.23.16), 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,
SummarizedExperiment
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, testthat, trackViewer, motifStack,
MMDiffBamSubset
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: 2016-05-16 02:10:51 UTC; biocbuild