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Last data update: 2014.03.03

ChIPpeakAnno

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

● BiocViews: Annotation, ChIPSeq, ChIPchip
● 12 images, 50 functions, 18 datasets
● Reverse Depends: 1

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPpeakAnno'
    finding HTML links ... done
    BED2RangedData                          html  
    ChIPpeakAnno-deprecated                 html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/ChIPpeakAnno-deprecated.Rd:50: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/ChIPpeakAnno-deprecated.Rd:51: missing file link 'RangedData'
    ChIPpeakAnno-package                    html  
    ExonPlusUtr.human.GRCh37                html  
    GFF2RangedData                          html  
    HOT.spots                               html  
    IDRfilter                               html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/IDRfilter.Rd:17: missing file link 'GRanges'
    Peaks.Ste12.Replicate1                  html  
    Peaks.Ste12.Replicate2                  html  
    Peaks.Ste12.Replicate3                  html  
    TSS.human.GRCh37                        html  
    TSS.human.GRCh38                        html  
    TSS.human.NCBI36                        html  
    TSS.mouse.GRCm38                        html  
    TSS.mouse.NCBIM37                       html  
    TSS.rat.RGSC3.4                         html  
    TSS.rat.Rnor_5.0                        html  
    TSS.zebrafish.Zv8                       html  
    TSS.zebrafish.Zv9                       html  
    addAncestors                            html  
    addGeneIDs                              html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/addGeneIDs.Rd:81: missing file link 'AnnotationDb'
    addMetadata                             html  
    annoGR                                  html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:71: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:72: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:72: missing file link 'EnsDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:80: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:27: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:36: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:37: missing file link 'EnsDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:56: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoGR.Rd:56: missing file link 'EnsDb'
    annoPeaks                               html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoPeaks.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annoPeaks.Rd:22: missing file link 'GRanges'
    annotatePeakInBatch                     html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annotatePeakInBatch.Rd:24: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annotatePeakInBatch.Rd:29: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/annotatePeakInBatch.Rd:88: missing file link 'GRanges'
    annotatedPeak                           html  
    assignChromosomeRegion                  html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/assignChromosomeRegion.Rd:24: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/assignChromosomeRegion.Rd:31: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/assignChromosomeRegion.Rd:38: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/assignChromosomeRegion.Rd:44: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/assignChromosomeRegion.Rd:70: missing file link 'TxDb'
    bdp                                     html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/bdp.Rd:15: missing file link 'GRanges'
    binOverFeature                          html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/binOverFeature.Rd:23: missing file link 'GRanges'
    bindist                                 html  
    condenseMatrixByColnames                html  
    convert2EntrezID                        html  
    countPatternInSeqs                      html  
    egOrgMap                                html  
    enrichedGO                              html  
    featureAlignedDistribution              html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedDistribution.Rd:17: missing file link 'SimpleRleList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedDistribution.Rd:17: missing file link 'RleList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedDistribution.Rd:20: missing file link 'GRanges'
    featureAlignedHeatmap                   html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedHeatmap.Rd:22: missing file link 'SimpleRleList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedHeatmap.Rd:22: missing file link 'RleList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedHeatmap.Rd:25: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedHeatmap.Rd:51: missing file link 'gList'
    featureAlignedSignal                    html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedSignal.Rd:16: missing file link 'SimpleRleList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedSignal.Rd:16: missing file link 'RleList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/featureAlignedSignal.Rd:19: missing file link 'GRanges'
    findEnhancers                           html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/findEnhancers.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/findEnhancers.Rd:22: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/findEnhancers.Rd:25: missing file link 'GRanges'
    findOverlappingPeaks                    html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/findOverlappingPeaks.Rd:71: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/findOverlappingPeaks.Rd:72: missing file link 'RangedData'
    findOverlapsOfPeaks                     html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/findOverlapsOfPeaks.Rd:19: missing file link 'GRanges'
    findVennCounts                          html  
    getAllPeakSequence                      html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/getAllPeakSequence.Rd:13: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/getAllPeakSequence.Rd:27: missing file link 'GRanges'
    getAnnotation                           html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/getAnnotation.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/getAnnotation.Rd:20: missing file link 'RangedData'
    getEnrichedGO                           html  
    getEnrichedPATH                         html  
    getGeneSeq                              html  
    getUniqueGOidCount                      html  
    getVennCounts                           html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/getVennCounts.Rd:17: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/getVennCounts.Rd:18: missing file link 'RangedData'
    hyperGtest                              html  
    makeVennDiagram                         html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/makeVennDiagram.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/makeVennDiagram.Rd:55: missing file link 'TxDb'
    mergePlusMinusPeaks                     html  
    myPeakList                              html  
    oligoFrequency                          html  
    oligoSummary                            html  
    peakPermTest                            html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/peakPermTest.Rd:22: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/peakPermTest.Rd:34: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/peakPermTest.Rd:41: missing file link 'TxDb'
    peaksNearBDP                            html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/peaksNearBDP.Rd:12: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/peaksNearBDP.Rd:13: missing file link 'RangedData'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/peaksNearBDP.Rd:15: missing file link 'GRanges'
    permPool                                html  
    pie1                                    html  
    preparePool                             html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/preparePool.Rd:17: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/preparePool.Rd:20: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/preparePool.Rd:38: missing file link 'GRanges'
    reCenterPeaks                           html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/reCenterPeaks.Rd:14: missing file link 'GRanges'
    summarizeOverlapsByBins                 html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:7: missing file link 'summarizeOverlaps'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:20: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:23: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:23: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:24: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:25: missing file link 'GAlignmentsList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:26: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:27: missing file link 'BamFileList'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:28: missing file link 'summarizeOverlaps'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:40: missing file link 'summarizeOverlaps'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:43: missing file link 'summarizeOverlaps'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizeOverlapsByBins.Rd:48: missing file link 'RangedSummarizedExperiment'
    summarizePatternInPeaks                 html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizePatternInPeaks.Rd:28: missing file link 'GRanges'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/summarizePatternInPeaks.Rd:28: missing file link 'RangedData'
    toGRanges                               html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/toGRanges.Rd:39: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/toGRanges.Rd:39: missing file link 'EnsDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/toGRanges.Rd:69: missing file link 'TxDb'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/toGRanges.Rd:73: missing file link 'GRanges'
    translatePattern                        html  
    wgEncodeTfbsV3                          html  
    write2FASTA                             html  
    xget                                    html  
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/xget.Rd:15: missing file link 'mget'
Rd warning: /tmp/Rtmp8ud6NX/R.INSTALL7c104d16fb8/ChIPpeakAnno/man/xget.Rd:26: missing file link 'mget'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChIPpeakAnno)
Making 'packages.html' ... done