API for htSeqTools
Quality Control, Visualization and Processing for High-Throughput Sequencing data

Global functions
PeakLocation Man page
PeakLocation,GRanges-method Man page
PeakLocation,RangedData-method Man page
PeakLocation,data.frame-method Man page
PeakLocation-methods Man page
PeakLocationBase Source code
[,gridCover,ANY,ANY,ANY-method Man page
alignPeaks Man page
alignPeaks,GRanges,character-method Man page
alignPeaks,GRangesList,ANY-method Man page
alignPeaks,GRangesList-method Man page
alignPeaks,IRangesList,list-method Man page
alignPeaks,RangedData,character-method Man page
alignPeaks,list,character-method Man page
alignPeaks-methods Man page
basesPerCut2dir Source code
cmds Man page
cmds,CompressedGRangesList-method Man page
cmds,GRangesList-method Man page
cmds,list-method Man page
cmds-methods Man page
cmdsFit Man page
cmdsFit,matrix-method Man page
cmdsFit-class Man page
cmdsFit-methods Man page
corRle Source code
corRleList Source code
countDifHitsWindow Source code
countHitsWindow Man page
countHitsWindow,GRanges-method Man page
countHitsWindow,RangedData-method Man page
countHitsWindow-methods Man page
coverageDiff Man page Source code
dist2midpnt Source code
enrichedChrRegions Man page
enrichedChrRegions,GRanges,GRanges-method Man page
enrichedChrRegions,GRanges,missing-method Man page
enrichedChrRegions,RangedData,RangedData-method Man page
enrichedChrRegions,RangedData,missing-method Man page
enrichedChrRegions-methods Man page
enrichedPeaks Man page
enrichedPeaks,GRanges,GRanges,GRanges-method Man page
enrichedPeaks,GRanges,GRanges,missing-method Man page
enrichedPeaks,GRanges,missing,missing-method Man page
enrichedPeaks,RangedData,IRanges,IRanges-method Man page
enrichedPeaks,RangedData,IRanges,missing-method Man page
enrichedPeaks,RangedData,IRangesList,IRangesList-method Man page
enrichedPeaks,RangedData,IRangesList,missing-method Man page
enrichedPeaks,RangedData,RangedData,RangedData-method Man page
enrichedPeaks,RangedData,RangedData,missing-method Man page
enrichedPeaks-methods Man page
enrichedRegions Man page
enrichedRegions,GRanges,GRanges,missing,ANY,ANY-method Man page
enrichedRegions,GRanges,missing,missing,ANY,ANY-method Man page
enrichedRegions,GRangesList,missing,missing,ANY,ANY-method Man page
enrichedRegions,RangedData,RangedData,missing,ANY,ANY-method Man page
enrichedRegions,RangedData,missing,missing,ANY,ANY-method Man page
enrichedRegions,list,missing,missing,ANY,ANY-method Man page
enrichedRegions,missing,missing,GRanges,ANY,ANY-method Man page
enrichedRegions,missing,missing,RangedData,ANY,missing-method Man page
enrichedRegions,missing,missing,RangedData,ANY,numeric-method Man page
enrichedRegions-methods Man page
extendRanges Man page
extendRanges,GRanges-method Man page
extendRanges,GRangesList-method Man page
extendRanges,RangedData-method Man page
extendRanges,list-method Man page
extendRanges-methods Man page
fdrEnrichedCounts Man page Source code
fillRleList Source code
filterDuplReads Man page
filterDuplReads,GRanges-method Man page
filterDuplReads,GRangesList-method Man page
filterDuplReads,RangedData-method Man page
filterDuplReads,list-method Man page
filterDuplReads-methods Man page
findPeakHeight Man page
findPeakHeight,GRanges,GRanges,GRanges-method Man page
findPeakHeight,RangedData,IRangesList,IRangesList-method Man page
findPeakHeight,RangedData,RangedData,RangedData-method Man page
findPeakHeight,RangedData,Rle,Rle-method Man page
findPeakHeight-methods Man page
getCover Man page
getCover,gridCover-method Man page
getGrid Source code
getGridList Source code
getViewsInfo Man page
getViewsInfo,gridCover-method Man page
giniCoverage Man page
giniCoverage,GRanges,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,GRanges,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,GRanges,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,GRanges,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,GRangesList,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,RangedData,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage,list,ANY,ANY,ANY,character,integer-method Man page
giniCoverage,list,ANY,ANY,ANY,character,missing-method Man page
giniCoverage,list,ANY,ANY,ANY,missing,integer-method Man page
giniCoverage,list,ANY,ANY,ANY,missing,missing-method Man page
giniCoverage-methods Man page
gridCover-class Man page
gridCoverage Man page Source code
hitsPerCut Source code
hitsPerCut2dir Source code
htSample Man page
ilogit Source code
islandCounts Man page
islandCounts,GRanges-method Man page
islandCounts,GRangesList-method Man page
islandCounts,RangedData-method Man page
islandCounts,list-method Man page
islandCounts-methods Man page
lines,gridCover-method Man page
listOverlap Man page
listOverlap,character,character,character,character-method Man page
listOverlap,character,character,missing,character-method Man page
listOverlap,factor,character,missing,missing-method Man page
listOverlap-methods Man page
logit Source code
meanRandomHits Source code
mergeRegions Man page
mergeRegions,GRanges-method Man page
mergeRegions,IRanges-method Man page
mergeRegions,RangedData-method Man page
mergeRegions,RleViews-method Man page
mergeRegions,data.frame-method Man page
mergeRegions,matrix-method Man page
mergeRegions-methods Man page
mergeRegionsCore Source code
plot,cmdsFit,ANY-method Man page
plot,cmdsFit-method Man page
plot,gridCover,ANY-method Man page
plot,gridCover-method Man page
plotChrRegions Man page Source code
plotMeanCoverage Man page
plotMeanCoverage,RleList,RangedData-method Man page
plotMeanCoverage-methods Man page
plotminHeight Man page Source code
randomHits2groups Source code
randomHitsWindow Source code
regionsCoverage Man page
regionsCoverage,ANY,ANY,ANY,RleList-method Man page
regionsCoverage-methods Man page
rowLogRegLRT Man page Source code
show,gridCover-method Man page
ssdCoverage Man page
ssdCoverage,GRanges-method Man page
ssdCoverage,GRangesList-method Man page
ssdCoverage,IRangesList-method Man page
ssdCoverage,RangedData-method Man page
ssdCoverage,list-method Man page
ssdCoverage-methods Man page
stdGrid Man page
stdGrid,gridCover-method Man page
stdGrid-methods Man page
stdPeakLocation Man page
stdPeakLocation,GRanges-method Man page
stdPeakLocation,RangedData-method Man page
stdPeakLocation,data.frame-method Man page
stdPeakLocation-methods Man page
stdPeakLocationBase Source code
tabDuplReads Man page
tabDuplReads,GRanges-method Man page
tabDuplReads,GRangesList-method Man page
tabDuplReads,RangedData-method Man page
tabDuplReads,list-method Man page
tabDuplReads-methods Man page
htSeqTools documentation built on Nov. 1, 2018, 2:04 a.m.