API for Bioconductor-mirror/ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Global functions
$,bindist-method Man page
$,permPool-method Man page
$<-,bindist-method Man page
$<-,permPool-method Man page
BED2RangedData Man page Source code
BED2RangedData-deprecated Man page
ChIPpeakAnno Man page
ChIPpeakAnno-deprecated Man page
ChIPpeakAnno-package Man page
EnsDb2GR Source code
ExonPlusUtr.human.GRCh37 Man page
GFF2RangedData Man page Source code
GFF2RangedData-deprecated Man page
HOT.spots Man page
IDRfilter Man page Source code
Peaks.Ste12.Replicate1 Man page
Peaks.Ste12.Replicate2 Man page
Peaks.Ste12.Replicate3 Man page
RangedData2GRanges Source code
TSS.human.GRCh37 Man page
TSS.human.GRCh38 Man page
TSS.human.NCBI36 Man page
TSS.mouse.GRCm38 Man page
TSS.mouse.NCBIM37 Man page
TSS.rat.RGSC3.4 Man page
TSS.rat.Rnor_5.0 Man page
TSS.zebrafish.Zv8 Man page
TSS.zebrafish.Zv9 Man page
TxDb2GR Source code
addAncestors Man page Source code
addGeneIDs Man page Source code
addMetadata Man page Source code
annoGR Man page
annoGR,EnsDb-method Man page
annoGR,GRanges-method Man page
annoGR,TxDb-method Man page
annoGR-class Man page
annoPeaks Man page Source code
annoScore Source code
annotatePeakInBatch Man page Source code
annotatedPeak Man page
assignChromosomeRegion Man page Source code
bdp Man page Source code
binOverFeature Man page Source code
binOverGene Man page Source code
binOverRegions Man page Source code
bindist Man page
bindist-class Man page
bindist-method Man page
buildBindingDistribution Source code
checkLoadedPackage Source code
cntOverlaps Source code
coerce,GRanges,annoGR-method Man page
coerce,annoGR,GRanges-method Man page
condenseMatrixByColnames Man page Source code
convert2EntrezID Man page Source code
countByOverlaps Source code
countPatternInSeqs Man page Source code
cumulativePercentage Man page Source code
df2GRanges Source code
egOrgMap Man page Source code
enrichedGO Man page
estFragmentLength Man page Source code
estLibSize Man page Source code
expandGR Source code
featureAlignedDistribution Man page Source code
featureAlignedExtendSignal Man page Source code
featureAlignedHeatmap Man page Source code
featureAlignedSignal Man page Source code
filterByLevel Source code
findEnhancers Man page Source code
findOverlappingPeaks Man page Source code
findOverlappingPeaks-deprecated Man page
findOverlapsOfPeaks Man page Source code
findVennCounts Man page Source code
formatSeqnames Source code
formatStrand Source code
getAllPeakSequence Man page Source code
getAnnotation Man page Source code
getEnrichedGO Man page Source code
getEnrichedPATH Man page Source code
getGOLevel Source code
getGeneSeq Man page Source code
getRelationship Source code
getUniqueGOidCount Man page Source code
getVennCounts Man page Source code
hyperGtest Man page Source code
info Man page
info,annoGR-method Man page
makeVennDiagram Man page Source code
mergePlusMinusPeaks Man page Source code
myPeakList Man page
newAGR Source code
newAnnoGR Source code
oligoFrequency Man page Source code
oligoSummary Man page Source code
overlappingPeaks Man page
overlappingPeaks-class Man page
peakPermTest Man page Source code
peaksNearBDP Man page Source code
permPool Man page
permPool-class Man page
permPool-method Man page
pie1 Man page Source code
plotBinOverRegions Man page Source code
preparePool Man page Source code
randPeaks Source code
ratio.zScore Source code
reCenterPeaks Man page Source code
removeAncestor Source code
runifGR Source code
summarizeOverlapsByBins Man page Source code
summarizePatternInPeaks Man page Source code
switchColNames Source code
tileCount Man page Source code
tileGRanges Man page Source code
toGRanges Man page
toGRanges,EnsDb-method Man page
toGRanges,RangedData-method Man page
toGRanges,TxDb-method Man page
toGRanges,character-method Man page
toGRanges,connection-method Man page
toGRanges,data.frame-method Man page
translatePattern Man page Source code
trimPeakList Source code
vennCounts Source code
wgEncodeTfbsV3 Man page
write2FASTA Man page Source code
xget Man page Source code
Bioconductor-mirror/ChIPpeakAnno documentation built on May 29, 2017, 2:09 a.m.