steveped/chipExtra
Additional functions for working with ChIP-Seq data

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Source code
81
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45
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steveped/chipExtra: Additional functions for working with ChIP-Seq data
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API

API for steveped/chipExtra
Additional functions for working with ChIP-Seq data

Global functions
.addAnnotations Source code
.addColourCol Source code
.addCols Source code
.addLabel Source code
.addLabels Source code
.addMcols Source code
.addRho Source code
.addXSide Source code
.addYSide Source code
.assignColours Source code
.assignLimits Source code
.calculateVoomWeights Source code
.checkArgsGrlToSe Source code
.checkCoverage Source code
.checkFeatures Source code
.checkGenes Source code
.checkHFGCArgs Source code
.checkMappingArgs Source code
.checkProfileDataFrames Source code
.coerceList Source code
.cols2Assays Source code
.ec_HMP Source code
.ec_HMP_adj Source code
.ec_bestTest Source code
.ec_combTests Source code
.ec_minTest Source code
.emptySE Source code
.importBedFile Source code
.importPeakFile Source code
.isValidBed Source code
.isValidBroad Source code
.isValidNarrow Source code
.makeCoverageTracks Source code
.makeFeatureTrack Source code
.makeFinalProfileHeatmap Man page Source code
.makeGeneTracks Source code
.makeHiCTrack Source code
.makeIdeoTrack Source code
.makeOLaps Source code
.makeSetSizes Source code
.make_GRCh37 Source code
.make_GRCh38 Source code
.make_GRCm38 Source code
.make_GRCm39 Source code
.make_T2T Source code
.make_hg19 Source code
.make_hg38 Source code
.make_mm10 Source code
.make_mm39 Source code
.mapFeatures Man page Source code
.mapGi Man page Source code
.mapHits Source code
.mapMcols2Ranges Source code
.mapWithin Man page Source code
.mcolnames Source code
.parseDotArgs Source code
.plotDoublePie Source code
.plotDoubleVenn Source code
.plotSinglePie Source code
.plotSingleVenn Source code
.plotTriplePie Source code
.plotTripleVenn Source code
.returnListColumn Source code
.se2DGEGLM Source code
.se2LT Source code
.se2Wald Source code
.unnest_by_col Source code
.voomChecks Source code
addDiffStatus Man page
addDiffStatus,DataFrame-method Man page
addDiffStatus,GRanges-method Man page
addDiffStatus,GRangesList-method Man page
addDiffStatus,SummarizedExperiment-method Man page
addDiffStatus,data.frame-method Man page
as_tibble Man page
as_tibble.DataFrame Man page Source code
as_tibble.GInteractions Man page Source code
as_tibble.GenomicRanges Man page Source code
as_tibble.Seqinfo Man page Source code
as_tibble.SummarizedExperiment Man page Source code
as_tibble.TopTags Man page Source code
bestOverlap Man page
bestOverlap,GRanges,GRanges-method Man page
bestOverlap,GRanges,GRangesList-method Man page
chopMC Man page Source code
colToRanges Man page
colToRanges,DataFrame-method Man page
colToRanges,GRanges-method Man page
colToRanges,data.frame-method Man page
collapseGenes Man page Source code
cytobands Man page
defineRegions Man page Source code
defineSeqinfo Man page Source code
distinctMC Man page Source code
dualFilter Man page Source code
ex_datasets Man page
ex_genes Man page
ex_hic Man page
ex_prom Man page
ex_trans Man page
extraChIPs Man page
extraChIPs-package Man page
fitAssayDiff Man page
fitAssayDiff,SummarizedExperiment-method Man page
fixed_width_datasets Man page
getProfileData Man page
getProfileData,BigWigFile,GenomicRanges-method Man page
getProfileData,BigWigFileList,GenomicRanges-method Man page
getProfileData,character,GenomicRanges-method Man page
grch37.cytobands Man page
grch38.cytobands Man page
grlToSE Man page
grlToSE,GRangesList-method Man page
importPeaks Man page Source code
intersectMC Man page
intersectMC,GRanges,GRanges-method Man page
makeConsensus Man page Source code
mapByFeature Man page Source code
mapGrlCols Man page Source code
mergeByCol Man page
mergeByCol,GenomicRanges-method Man page
mergeByCol,RangedSummarizedExperiment-method Man page
mergeByHMP Man page
mergeByHMP,GenomicRanges-method Man page
mergeByHMP,RangedSummarizedExperiment-method Man page
mergeBySig Man page
mergeBySig,GenomicRanges-method Man page
mergeBySig,RangedSummarizedExperiment-method Man page
partitionRanges Man page
partitionRanges,GRanges,GRanges-method Man page
peaks Man page
plotAssayDensities Man page
plotAssayDensities,SummarizedExperiment-method Man page
plotAssayHeatmap Man page
plotAssayHeatmap,SummarizedExperiment-method Man page
plotAssayPCA Man page
plotAssayPCA,SummarizedExperiment-method Man page
plotAssayRle Man page
plotAssayRle,SummarizedExperiment-method Man page
plotGrlCol Man page Source code
plotHFGC Man page Source code
plotOverlaps Man page
plotOverlaps,GRangesList-method Man page
plotOverlaps,list-method Man page
plotPairwise Man page Source code
plotPie Man page
plotPie,DataFrame-method Man page
plotPie,GRanges-method Man page
plotPie,data.frame-method Man page
plotProfileHeatmap Man page
plotProfileHeatmap,GenomicRanges-method Man page
plotProfileHeatmap,GenomicRangesList-method Man page
plotSplitDonut Man page
plotSplitDonut,DataFrame-method Man page
plotSplitDonut,GRanges-method Man page
plotSplitDonut,data.frame-method Man page
propOverlap Man page
propOverlap,GRanges,GRanges-method Man page
reduceMC Man page Source code
se Man page
setdiffMC Man page
setdiffMC,GRanges,GRanges-method Man page
setoptsMC Man page
stitchRanges Man page Source code
unionMC Man page
unionMC,GRanges,GRanges-method Man page
voomWeightsFromCPM Man page Source code
steveped/chipExtra documentation built on May 2, 2024, 12:11 p.m.

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