Repitools
Epigenomic tools

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337
Source code
60
Man pages
67
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API for Repitools
Epigenomic tools

Global functions
.belongsTo Source code
.cpgBoxplots Source code
.createBins Source code
.diracBetaDirac Source code
.dlogit Source code
.doBiasPlot Source code
.doChrPlot Source code
.drawSegs Source code
.eqn2 Source code
.eqn3 Source code
.fdrTable Source code
.getBed Source code
.getCpu Source code
.getNames Source code
.getQuantile Source code
.getRegions Source code
.getRegionsChr Source code
.getcredible Source code
.getcredibleDBD Source code
.ineqn Source code
.ineqn2 Source code
.invlogit Source code
.logit Source code
.makeClusters Source code
.makeImageRect Source code
.mappabilityBSGenome Source code
.mappabilityBigWig Source code
.mappabilityFASTA Source code
.marg Source code
.margDirac Source code
.margDirac_fB Source code
.margDirac_fW Source code
.methylEstDBD Source code
.methylEstbeta Source code
.mycdf Source code
.mydmarginal Source code
.mydmarginalDBD Source code
.myhpd Source code
.myoptimize Source code
.myoptimizeDirac Source code
.myquantile Source code
.plotFreqs Source code
.regionStats Source code
.scoreIntensity Source code
AdjustedCopyEstimate Man page
AdjustedCopyEstimate,numeric,GRanges,numeric,numeric,matrix,list Man page
AdjustedCopyEstimate-class Man page
AffymetrixCdfFile Man page
AffymetrixCdfFile-class Man page
AffymetrixCelSet Man page
AffymetrixCelSet-class Man page
BAM2GRanges Man page
BAM2GRanges,character-method Man page
BAM2GRangesList Man page
BAM2GRangesList,character-method Man page
Basic_Statistics Man page
Basic_Statistics,FastQC-method Man page
Basic_Statistics,SequenceQC-method Man page
Basic_Statistics,SequenceQCSet-method Man page
BayMethList Man page
BayMethList,GRanges,matrix,matrix,numeric-method Man page
BayMethList-class Man page
ChromaBlocks Man page
ChromaBlocks,GRangesList,GRangesList-method Man page
ChromaResults Man page
ChromaResults-class Man page
ClusteredScoresList Man page
ClusteredScoresList,ScoresList-method Man page
ClusteredScoresList-class Man page
CopyEstimate Man page
CopyEstimate,GRanges,matrix,GRangesList,character-method Man page
CopyEstimate-class Man page
FDRTable Man page
FDRTable,ChromaResults-method Man page
FastQC-class Man page
GCAdjustParams Man page
GCAdjustParams,BSgenome,MappabilitySource-method Man page
GCAdjustParams-class Man page
GCadjustCopy Man page
GCadjustCopy,GRanges,matrix,GCAdjustParams-method Man page
GCadjustCopy,data.frame,matrix,GCAdjustParams-method Man page
GCbiasPlots Man page
GCbiasPlots,AdjustedCopyEstimate-method Man page
MappabilitySource Man page
MappabilitySource-class Man page
MismatchTable Man page
MismatchTable,SequenceQC-method Man page
MismatchTable,SequenceQCSet-method Man page
Mismatches Man page
Mismatches,SequenceQC-method Man page
Mismatches,SequenceQCSet-method Man page
Overrepresented_sequences Man page
Overrepresented_sequences,FastQC-method Man page
Overrepresented_sequences,SequenceQC-method Man page
Overrepresented_sequences,SequenceQCSet-method Man page
Per_base_GC_content Man page
Per_base_GC_content,FastQC-method Man page
Per_base_GC_content,SequenceQC-method Man page
Per_base_GC_content,SequenceQCSet-method Man page
Per_base_N_content Man page
Per_base_N_content,FastQC-method Man page
Per_base_N_content,SequenceQC-method Man page
Per_base_N_content,SequenceQCSet-method Man page
Per_base_sequence_content Man page
Per_base_sequence_content,FastQC-method Man page
Per_base_sequence_content,SequenceQC-method Man page
Per_base_sequence_content,SequenceQCSet-method Man page
Per_base_sequence_quality Man page
Per_base_sequence_quality,FastQC-method Man page
Per_base_sequence_quality,SequenceQC-method Man page
Per_base_sequence_quality,SequenceQCSet-method Man page
Per_sequence_GC_content Man page
Per_sequence_GC_content,FastQC-method Man page
Per_sequence_GC_content,SequenceQC-method Man page
Per_sequence_GC_content,SequenceQCSet-method Man page
Per_sequence_quality_scores Man page
Per_sequence_quality_scores,FastQC-method Man page
Per_sequence_quality_scores,SequenceQC-method Man page
Per_sequence_quality_scores,SequenceQCSet-method Man page
QdnaData Man page Source code
QdnaData-class Man page
RegionStats-class Man page
ScoresList Man page
ScoresList-class Man page
SequenceQC-class Man page
SequenceQCSet Man page
SequenceQCSet-class Man page
Sequence_Duplication_Levels Man page
Sequence_Duplication_Levels,FastQC-method Man page
Sequence_Duplication_Levels,SequenceQC-method Man page
Sequence_Duplication_Levels,SequenceQCSet-method Man page
Sequence_Length_Distribution Man page
Sequence_Length_Distribution,FastQC-method Man page
Sequence_Length_Distribution,SequenceQC-method Man page
Sequence_Length_Distribution,SequenceQCSet-method Man page
[,BayMethList,ANY,missing,ANY-method Man page
[,ClusteredScoresList,ANY,missing,ANY-method Man page
[,ScoresList,ANY,missing,ANY-method Man page
[,SequenceQCSet,ANY,missing,ANY-method Man page
abcdDNA Man page Source code
absoluteCN Man page
absoluteCN,GRanges,matrix,GCAdjustParams-method Man page
absoluteCN,data.frame,matrix,GCAdjustParams-method Man page
annoDF2GR Man page
annoDF2GR,data.frame-method Man page
annoGR2DF Man page
annoGR2DF,GRanges-method Man page
annotationBlocksCounts Man page
annotationBlocksCounts,ANY,data.frame-method Man page
annotationBlocksCounts,GRanges,GRanges-method Man page
annotationBlocksCounts,GRangesList,GRanges-method Man page
annotationBlocksCounts,character,GRanges-method Man page
annotationBlocksLookup Man page
annotationBlocksLookup,data.frame,GRanges-method Man page
annotationBlocksLookup,data.frame,data.frame-method Man page
annotationCounts Man page
annotationCounts,ANY,GRanges-method Man page
annotationCounts,ANY,data.frame-method Man page
annotationLookup Man page
annotationLookup,data.frame,GRanges-method Man page
annotationLookup,data.frame,data.frame-method Man page
binPlots Man page
binPlots,ScoresList-method Man page
blocks Man page
blocks,ChromaResults-method Man page
blocksStats Man page
blocksStats,ANY,GRanges-method Man page
blocksStats,ANY,data.frame-method Man page
checkProbes Man page
checkProbes,GRanges,GRanges-method Man page
checkProbes,data.frame,data.frame-method Man page
chr21genes Man page
chromosomeCNplots Man page
chromosomeCNplots,AdjustedCopyEstimate-method Man page
chromosomeCNplots,CopyEstimate-method Man page
class:ChromaResults Man page
class:FastQC Man page
class:QdnaData Man page
class:RegionStats Man page
class:SequenceQC Man page
class:SequenceQCSet Man page
clusterPlots Man page
clusterPlots,ClusteredScoresList-method Man page
clusterPlots,ScoresList-method Man page
clusters Man page
clusters,ClusteredScoresList-method Man page
control Man page
control,BayMethList-method Man page
control<- Man page
control<-,BayMethList-method Man page
cpgBoxplots Man page
cpgBoxplots,AffymetrixCelSet-method Man page
cpgBoxplots,matrix-method Man page
cpgDens Man page
cpgDens,BayMethList-method Man page
cpgDens<- Man page
cpgDens<-,BayMethList-method Man page
cpgDensityCalc Man page
cpgDensityCalc,GRanges,BSgenome-method Man page
cpgDensityCalc,GRangesList,BSgenome-method Man page
cpgDensityCalc,data.frame,BSgenome-method Man page
cpgDensityPlot Man page
cpgDensityPlot,GRangesList-method Man page
cutoff Man page
cutoff,ChromaResults-method Man page
determineOffset Man page Source code
empBayes Man page Source code
enrichmentCalc Man page
enrichmentCalc,GRanges-method Man page
enrichmentCalc,GRangesList-method Man page
enrichmentPlot Man page
enrichmentPlot,GRangesList-method Man page
expr Man page
fOffset Man page
fOffset,BayMethList-method Man page
fOffset<- Man page
fOffset<-,BayMethList-method Man page
featureBlocks Man page
featureBlocks,GRanges-method Man page
featureBlocks,data.frame-method Man page
featureScores Man page
featureScores,ANY,GRanges-method Man page
featureScores,ANY,data.frame-method Man page
findClusters Man page Source code
gcContentCalc Man page
gcContentCalc,GRanges,BSgenome-method Man page
gcContentCalc,data.frame,BSgenome-method Man page
genQC Man page
genQC,SequenceQCSet-method Man page
genQC,character-method Man page
genomeBlocks Man page
genomeBlocks,BSgenome-method Man page
genomeBlocks,numeric-method Man page
getProbePositionsDf Man page
getProbePositionsDf,AffymetrixCdfFile-method Man page
getSampleOffsets Man page Source code
hcRegions Man page
hyperg2F1_vec Man page Source code
length Man page
length,BayMethList-method Man page
length,ScoresList-method Man page
loadPairFile Man page Source code
loadSampleDirectory Man page Source code
makeWindowLookupTable Man page Source code
mappabilityCalc Man page
mappabilityCalc,GRanges,MappabilitySource-method Man page
mappabilityCalc,data.frame,MappabilitySource-method Man page
maskEmpBayes Man page
maskEmpBayes,BayMethList-method Man page
maskEmpBayes<- Man page
maskEmpBayes<-,BayMethList-method Man page
maskOut Man page Source code
mergeReplicates Man page
mergeReplicates,GRangesList-method Man page
methEst Man page
methEst,BayMethList-method Man page
methEst<- Man page
methEst<-,BayMethList-method Man page
methylEst Man page Source code
multiHeatmap Man page Source code
names,ScoresList-method Man page
names<-,ScoresList-method Man page
ncontrol Man page
ncontrol,BayMethList-method Man page
nsampleInterest Man page
nsampleInterest,BayMethList-method Man page
plotClusters Man page
plotClusters,GRanges-method Man page
plotClusters,data.frame-method Man page
plotQdnaByCN Man page Source code
priorTab Man page
priorTab,BayMethList-method Man page
priorTab<- Man page
priorTab<-,BayMethList-method Man page
processNDF Man page Source code
profilePlots Man page
profilePlots,ScoresList-method Man page
readFastQC Man page Source code
regionStats Man page
regionStats,AffymetrixCelSet-method Man page
regionStats,matrix-method Man page
regions Man page
regions,ChromaResults-method Man page
relativeCN Man page
relativeCN,GRanges,matrix-method Man page
relativeCN,data.frame,matrix-method Man page
sampleInterest Man page
sampleInterest,BayMethList-method Man page
sampleInterest<- Man page
sampleInterest<-,BayMethList-method Man page
samplesList Man page
sequenceCalc Man page
sequenceCalc,GRanges,BSgenome-method Man page
sequenceCalc,data.frame,BSgenome-method Man page
setCNVOffsets Man page Source code
show,AdjustedCopyEstimate-method Man page
show,BayMethList-method Man page
show,ChromaResults-method Man page
show,ClusteredScoresList-method Man page
show,CopyEstimate-method Man page
show,FastQC-method Man page
show,QdnaData-method Man page
show,RegionStats-method Man page
show,ScoresList-method Man page
show,SequenceQC-method Man page
show,SequenceQCSet-method Man page
subsetRows Man page
subsetRows,ClusteredScoresList-method Man page
subsetRows,ScoresList-method Man page
summarizeScores Man page
summarizeScores,ScoresList,matrix-method Man page
tables Man page
tables,ScoresList-method Man page
windows Man page
windows,BayMethList-method Man page
windows<- Man page
windows<-,BayMethList-method Man page
writeWig Man page
writeWig,AffymetrixCelSet-method Man page
writeWig,GRangesList-method Man page
Repitools documentation built on Nov. 8, 2020, 7:52 p.m.

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