API for Pasha
Preprocessing of Aligned Sequences from HTS Analyses

Global functions
.testFunctional	Man page
.testFunctionalMultiread	Man page
.testFunctionalMultiread_generateResults	Man page
.testFunctional_generateResults	Man page
AlignedData	Man page
AlignedData-class	Man page
AnalyzeRepeat	Man page
CSEMDispatch	Man page
C_binVector	Man page
C_elongationEstimation	Man page
C_pileupDouble	Man page
Pasha	Man page
Pasha-package	Man page
RemoveArtifact	Man page
UniformDispatch	Man page
WigRepeatAnalyzer	Man page
[,AlignedData,ANY,ANY-method	Man page
binVector	Man page
checkPairsOK	Man page
checkPairsOK,AlignedData-method	Man page
cleanNonSimplePairs	Man page
cleanNonSimplePairs,AlignedData-method	Man page
dropChromosomePattern	Man page
dropChromosomePattern,AlignedData-method	Man page
dropUndefinedStrand	Man page
dropUndefinedStrand,AlignedData-method	Man page
elongationEstimation	Man page
estimateElongationSize	Man page
filterInsertSize	Man page
filterInsertSize,AlignedData-method	Man page
filterReadSize	Man page
filterReadSize,AlignedData-method	Man page
flag	Man page
flag,AlignedData-method	Man page
flag<-	Man page
flag<-,AlignedData-method	Man page
generatePiled	Man page
getArtefactsIndexes	Man page
getOrphansIndexes	Man page
getOrphansIndexes,AlignedData-method	Man page
getStats,AlignedData-method	Man page
initialize	Man page
isize	Man page
isize,AlignedData-method	Man page
isize<-	Man page
isize<-,AlignedData-method	Man page
length	Man page
length,AlignedData-method	Man page
mapq	Man page
mapq,AlignedData-method	Man page
mapq<-	Man page
mapq<-,AlignedData-method	Man page
mergeWigs	Man page
mrnm	Man page
mrnm,AlignedData-method	Man page
mrnm<-	Man page
mrnm<-,AlignedData-method	Man page
multiread_CSEMDispatch	Man page
multiread_RemoveArtifact	Man page
multiread_UniformDispatch	Man page
normAndSubtractWIG	Man page
normalizeChrNames	Man page
normalizeChrNames,AlignedData-method	Man page
notAligned	Man page
notAligned,AlignedData-method	Man page
notAligned<-	Man page
notAligned<-,AlignedData-method	Man page
pairedEnds	Man page
pairedEnds,AlignedData-method	Man page
pairedEnds<-	Man page
pairedEnds<-,AlignedData-method	Man page
pileupDouble	Man page
plotReadsRepartitionAnnotations	Man page
position	Man page
position,AlignedData-method	Man page
position<-	Man page
position<-,AlignedData-method	Man page
processPipeline	Man page
qwidth	Man page
qwidth,AlignedData-method	Man page
qwidth<-	Man page
qwidth<-,AlignedData-method	Man page
readAlignedData	Man page
readID	Man page
readID,AlignedData-method	Man page
readID<-	Man page
readID<-,AlignedData-method	Man page
readMultipleAlignedData	Man page
readWIG	Man page
seqnames	Man page
seqnames,AlignedData-method	Man page
seqnames<-	Man page
seqnames<-,AlignedData-method	Man page
sortByPairs	Man page
sortByPairs,AlignedData-method	Man page
strand	Man page
strand,AlignedData-method	Man page
strand<-	Man page
strand<-,AlignedData-method	Man page
weight	Man page
weight,AlignedData-method	Man page
weight<-	Man page
weight<-,AlignedData-method	Man page
writeWIG	Man page