API for robertdouglasmorrison/DuffyNGS
Duffy Lab NGS Analysis Pipeline for RNA-seq, ChIP-seq, and DNA-seq

Global functions
AAcountsToPercents Source code
BAM.fieldTable Man page
BAM.index Man page
BAM.indexFASTA Man page
BAM.merge Man page
BAM.mpileup Man page
BAM.sort Man page
BAM.verifySorted Man page
BAM_Files Man page
CP_cleanup Source code
CPplotter Source code
CR_cleanup Source code
CRblaster Source code
CRplotter Source code
DuffyNGS Man page
DuffyNGS-package Man page
DuffyNGS_Annotation Man page
DuffyNGS_Options Man page
MPU.callBases Man page Source code
MPU.callMatrixToBaseCounts Man page
MPU.callStringToTable Man page Source code
MPU.callStringsToMatrix Man page Source code
MPU.callTableToString Man page Source code
MPU.strandDepth Man page Source code
MPU.tablifyIndelCalls Source code
SAM2BAM Man page
VCF.HighScoreDepth Source code
VCF.Pvalue Source code
VCF.Score Source code
VCF.TotalDepth Source code
addOneUSPtoCPT Source code
addOneUSRtoCRT Source code
addPairSetsToCPT Source code
addPairSetsToCRT Source code
alignQual Man page Man page
alignQual,bamAlign-method Man page
alignQual,bamRange-method Man page
alignQual-methods Man page Man page
alignSeq Man page Man page
alignSeq,bamAlign-method Man page
alignSeq,bamRange-method Man page
alignSeq-methods Man page Man page
alignToWig Man page
as.0.100.percent Source code
as.data.frame.bamRange Man page Source code
as.data.frame.refSeqDict Source code
as.readAntisense Source code
as.readSense Source code
asDistanceMatrix Source code
autoRunCR Source code
averageIsolatePercents Source code
bamAlign-class Man page
bamClose,bamReader-method Man page
bamCopy Man page
bamCopy,bamReader-method Man page
bamCopy-methods Man page
bamHeaderText Source code
bamRange Man page Source code
bamRange-class Man page
bamReadStats Man page
bamReader Man page Source code
bamReader-class Man page
bamSave,bamReader-method Man page
bamSort Man page
bamSort,bamReader-method Man page
baseConsensusFromBCM Source code
basePercentsFromBCM Source code
blankBCM Source code
blankRCM Source code
bowtie2Par Man page Source code
bowtie2Par.defaults Man page Source code
bowtiePar Source code
bowtiePar.defaults Source code
buildAllAnnotationFiles Man page
buildBowtie2BuildCommandLine Man page
buildBowtie2CommandLine Man page
buildRiboClearingFiles Man page
buildSpliceJunctionFiles Man page
buildUSPfromFile Source code
buildUSRfromFile Source code
calc2CPalignment Source code
calc2CRalignment Source code
calc2USPalignment Source code
calc2USRalignment Source code
calcOneSeqPctDistance Source code
calcOneSeqPctPvalue Source code
callBowtie Man page
callBowtie2 Man page
callTable.Pvalue Source code
callTable.totalSum Source code
checkBowtie2Version Man page
cigarData Man page
cigarData,bamAlign-method Man page
cigarData-methods Man page
cleanupBAMfiles Man page Source code
cleanupHLAtypingFiles Source code
cleanupVelvetFiles Source code
coerce,bamRange,data.frame-method Man page
combine2CP Source code
combine2CR Source code
combineAndReduceCPT Source code
combineAndReduceCRT Source code
compressSpliceMaps Man page
create.index Man page
create.index,bamReader-method Man page
create.index-methods Man page
dashedLine Source code
drawOnePeptide Source code
drawOneRead Source code
evaluateALIGNstats Source code
evaluateBaseFlips Source code
evaluateGeneStats Source code
evaluateIndels Source code
evaluateMARstats Source code
evaluateSeqStats Source code
expandToFitMSA Source code
extractBlastXMLdetails Source code
extractOneXMLiterationSet Source code
extractPipelineSummaryDetails Man page
failedQC Man page
failedQC,bamAlign-method Man page
failedQC-methods Man page
failedQC<- Man page
failedQC<-,bamAlign-method Man page
failedQC<--methods Man page
fastCS2DNA Source code
fastSRO Source code
fastqReadStats Man page
fastqToBAM Man page
filename,bamReader-method Man page
findFreeSpot Source code Source code
firstInPair Man page
firstInPair,bamAlign-method Man page
firstInPair-methods Man page
firstInPair<- Man page
firstInPair<-,bamAlign-method Man page
firstInPair<--methods Man page
flag Man page
flag,bamAlign-method Man page
flag-methods Man page
flag<- Man page
flag<-,bamAlign-method Man page
flag<--methods Man page
freeCPTpairs Source code
freeCRTpairs Source code
freeOneCPT Source code
freeOneCRT Source code
gapShiftCP Source code
gapShiftCR Source code
genePlotWithContigs Source code
getAlignmentOffsetAndGap Source code Source code
getAllTags Man page
getAllTags,bamAlign-method Man page
getAllTags-methods Man page
getBestCPTalignment Source code
getBestCRTalignment Source code
getBowtie2AlignMetrics Man page
getBowtie2Version Man page Man page
getHeader,bamReader-method Man page
getHeaderText,bamReader-method Man page
getNextAlign,bamRange-method Man page
getNextAlign,bamReader-method Man page
getPrevAlign Man page
getPrevAlign,bamRange-method Man page
getPrevAlign-methods Man page
getRawFastqFileNames Source code
getReadSense Source code
getRefCoords Man page
getRefCoords,bamReader-method Man page
getRefCoords-methods Man page
getRefCount Man page
getRefCount,bamReader-method Man page
getRefCount-methods Man page
getRefData Man page
getRefData,bamReader-method Man page
getRefData-methods Man page
getTag Man page
getTag,bamAlign-method Man page
getTag-methods Man page
getUSPentry Source code
getUSRentry Source code
graphVelvetContigSurvey Source code
inUseCPTpairs Source code
inUseCPTs Source code
inUseCRTpairs Source code
inUseCRTs Source code
index.initialized Man page
index.initialized,bamReader-method Man page
index.initialized-methods Man page
initialize,bamAlign-method Man page
initialize,bamRange-method Man page
initialize,bamReader-method Man page
insertPastCurrent Man page
insertPastCurrent,bamRange-method Man page
insertPastCurrent-methods Man page
insertPreCurrent Man page
insertPreCurrent,bamRange-method Man page
insertPreCurrent-methods Man page
insertSize Man page
insertSize,bamAlign-method Man page
insertSize-methods Man page
interestingContigs Source code
isOpen,bamReader-method Man page
load.index Man page
load.index,bamReader-method Man page
mapQuality Man page
mapQuality,bamAlign-method Man page
mapQuality-methods Man page
massageHitDefinition Source code
matePosition Man page
matePosition,bamAlign-method Man page
matePosition-methods Man page
mateRefID Man page
mateRefID,bamAlign-method Man page
mateRefID-methods Man page
mateReverseStrand Man page
mateReverseStrand,bamAlign-method Man page
mateReverseStrand-methods Man page
mateReverseStrand<- Man page
mateReverseStrand<-,bamAlign-method Man page
mateReverseStrand<--methods Man page
mateUnmapped Man page
mateUnmapped,bamAlign-method Man page
mateUnmapped-methods Man page
mateUnmapped<- Man page
mateUnmapped<-,bamAlign-method Man page
mateUnmapped<--methods Man page
measureSequenceDifference Source code
measureSequenceDistances Source code
measureSequenceVariation Source code
mergeALIGNstats Source code
mergeBaseStats Source code
mergeGeneStats Source code
mergeIndelStats Source code
mergeMARstats Source code
mergePeptideFiles Source code
mergeSeqStats Source code
moveCurrentAlign Man page
moveCurrentAlign,bamRange-method Man page
moveCurrentAlign-methods Man page
multiPosition.plotSNP Source code
multiSample.plotSNP Source code
nCigar Man page
nCigar,bamAlign-method Man page
nCigar-methods Man page
newBCM Source code
newCP Source code
newCPT Source code
newCR Source code
newCRT Source code
newRCM Source code
newUSP Source code
newUSR Source code
onUnload Source code
overlayContigs Source code
paired Man page
paired,bamAlign-method Man page
paired-methods Man page
paired<- Man page
paired<-,bamAlign-method Man page
paired<--methods Man page
pcrORopt_duplicate Man page
pcrORopt_duplicate,bamAlign-method Man page
pcrORopt_duplicate-methods Man page
pcrORopt_duplicate<- Man page
pcrORopt_duplicate<-,bamAlign-method Man page
pcrORopt_duplicate<--methods Man page
peakScoreROC Source code
phredScoreCP Source code
phredScoreCR Source code
pipe.AlignStats Man page
pipe.AlignToWig Man page
pipe.Alignment Man page
pipe.AlignmentPie Man page
pipe.BAMpileup Man page
pipe.BuildSNP.FreqMatrix Source code
pipe.ChIPalignment Man page
pipe.ChIPpeaks Man page
pipe.ChIPseq Man page
pipe.DESeq Man page
pipe.DNAalignment Man page
pipe.DNAseq Man page
pipe.DiffExpression Man page
pipe.EdgeR Man page
pipe.ExtractPipelineSummaryDetails Man page
pipe.GenomicAlign Man page
pipe.MARsurvey Source code
pipe.MetaResults Man page
pipe.PlotGene Man page
pipe.PlotSNP Man page
pipe.PostAlignTasks Man page
pipe.PreAlignTasks Man page
pipe.QuickQC Man page
pipe.RIPalignment Man page
pipe.RIPpeaks Man page
pipe.RIPpeaksToAltGeneMap Man page
pipe.RIPseq Man page
pipe.RNAalignment Man page
pipe.RNAseq Man page
pipe.RankProduct Man page
pipe.RiboClear Man page
pipe.RoundRobin Man page
pipe.SAM Man page
pipe.SpliceAlign Man page
pipe.TranscriptCluster Man page
pipe.TranscriptToHTML Man page
pipe.Transcriptome Man page
pipe.VariantCalls Man page
pipe.VariantSummary Man page Source code
pipeline Man page
plotAlignScoreData Source code
plotAlignStats Source code
plotBaseStatData Source code
plotGeneStatData Source code
plotIndelStatData Source code
plotMARstatData Source code
plotOneCPT Source code
plotOneCPTpair Source code
plotOneCRT Source code
plotOneCRTpair Source code
plotSNP Source code
plotSeqStatData Source code
plotTwoCP Source code
plotTwoCR Source code
pop_back Man page
pop_back,bamRange-method Man page
pop_back-methods Man page
pop_front Man page
pop_front,bamRange-method Man page
pop_front-methods Man page
position Man page Man page
position,bamAlign-method Man page
position,bamRange-method Man page
position-methods Man page Man page
properPair Man page
properPair,bamAlign-method Man page
properPair-methods Man page
properPair<- Man page
properPair<-,bamAlign-method Man page
properPair<--methods Man page
proteinConstructPileupSummary Source code
push_back Man page
push_back,bamRange-method Man page
push_back-methods Man page
push_front Man page
push_front,bamRange-method Man page
push_front-methods Man page
rankVelvetContigSurvey Source code
readID Man page Man page
readID,bamAlign-method Man page
readID,bamRange-method Man page
readID-methods Man page Man page
readQual Man page Man page
readQual,bamAlign-method Man page
readQual,bamRange-method Man page
readQual-methods Man page Man page
readSeq Man page Man page
readSeq,bamAlign-method Man page
readSeq,bamRange-method Man page
readSeq-methods Man page Man page
readStats Man page
readplotCP Source code
readplotCR Source code
refID Man page Man page
refID,bamAlign-method Man page
refID,bamRange-method Man page
refID-methods Man page Man page
refID2seqID Source code
renameFileContents Source code
residueConsensusFromRCM Source code
residuePercentsFromRCM Source code
revCompBCM Source code
revCompCR Source code
revCompCRcolors Source code
reverseStrand Man page Man page
reverseStrand,bamAlign-method Man page
reverseStrand,bamRange-method Man page
reverseStrand-methods Man page Man page
reverseStrand<- Man page
reverseStrand<-,bamAlign-method Man page
reverseStrand<--methods Man page
rewind Man page
rewind,bamRange-method Man page
rewind,bamReader-method Man page
rewind-methods Man page
runCP Source code
runCR Source code
runDiffExpression Man page
saveCPTcontext Source code
saveCRTcontext Source code
saveUSPcontext Source code
saveUSRcontext Source code
secondInPair Man page
secondInPair,bamAlign-method Man page
secondInPair-methods Man page
secondInPair<- Man page
secondInPair<-,bamAlign-method Man page
secondInPair<--methods Man page
secondaryAlign Man page
secondaryAlign,bamAlign-method Man page
secondaryAlign-methods Man page
secondaryAlign<- Man page
secondaryAlign<-,bamAlign-method Man page
secondaryAlign<--methods Man page
seqID2refID Source code
showCGpct Source code
size Man page
size,bamRange-method Man page
size-methods Man page
stepNextAlign Man page
stepNextAlign,bamRange-method Man page
stepNextAlign-methods Man page
stepPrevAlign Man page
stepPrevAlign,bamRange-method Man page
stepPrevAlign-methods Man page
testAll Source code
testBCM Source code
testCP Source code
testCPT Source code
testCR Source code
testCRT Source code
testRCM Source code
unmapped Man page
unmapped,bamAlign-method Man page
unmapped-methods Man page
unmapped<- Man page
unmapped<-,bamAlign-method Man page
unmapped<--methods Man page
visualizeGroupDifference Source code
writeCurrentAlign Man page
writeCurrentAlign,bamRange-method Man page
writeCurrentAlign-methods Man page
writeUSPasFasta Source code
writeUSRasFasta Source code
robertdouglasmorrison/DuffyNGS documentation built on Jan. 11, 2019, 5:37 p.m.