.addPercent	dot-addPercent
.emptyPlot	dot-emptyPlot
.FastpFile-class	dot-FastpFile-class
.FastqcFile-class	dot-FastqcFile-class
.getToolName	dot-getToolName
.hidePWFRects	dot-hidePWFRects
.makeDendro	dot-makeDendro
.makeLabels	dot-makeLabels
.makePwfGradient	dot-makePwfGradient
.makeSidebar	dot-makeSidebar
.parseAdapterRemovalLogs	dot-parseAdapterRemovalLogs
.parseBowtieLogs	dot-parseBowtieLogs
.parseBuscoLogs	dot-parseBuscoLogs
.parseCutadaptLogs	dot-parseCutadaptLogs
.parseDuplicationMetricsLogs	dot-parseDuplicationMetricsLogs
.parseFeatureCountsLogs	dot-parseFeatureCountsLogs
.parseFlagstatLogs	dot-parseFlagstatLogs
.parseHisat2Logs	dot-parseHisat2Logs
.parseMacs2CallpeakLogs	dot-parseMacs2CallpeakLogs
.parseQuastLogs	dot-parseQuastLogs
.parseRnaseqcMetricsLogs	dot-parseRnaseqcMetricsLogs
.parseSalmonLibFormatCountsLogs	dot-parseSalmonLibFormatCountsLogs
.parseSalmonMetaInfoLogs	dot-parseSalmonMetaInfoLogs
.parseStarLogs	dot-parseStarLogs
.parseTrimmomaticLogs	dot-parseTrimmomaticLogs
.parseUmitoolsDedupLogs	dot-parseUmitoolsDedupLogs
.prepHeatmap	dot-prepHeatmap
.renderDendro	dot-renderDendro
.splitByTab	dot-splitByTab
.updateThemeFromDots	dot-updateThemeFromDots
estGcDistn	estGcDistn
estGcDistn,ANY-method	estGcDistn
estGcDistn,character-method	estGcDistn
estGcDistn,DNAStringSet-method	estGcDistn
FastpData	FastpData
FastpData-class	FastpData
FastpDataList	FastpDataList
FastpDataList-class	FastpDataList
FastqcData	FastqcData
FastqcData-class	FastqcData
FastqcDataList	FastqcDataList
FastqcDataList-class	FastqcDataList
fqcVersion	fqcVersion
fqcVersion,ANY-method	fqcVersion
fqcVersion,FastqcData-method	fqcVersion
fqcVersion,FastqcDataList-method	fqcVersion
fqName	fqName-methods
fqName,ANY-method	fqName-methods
fqName,FastpData-method	fqName-methods
fqName,FastpDataList-method	fqName-methods
fqName,FastqcData-method	fqName-methods
fqName,FastqcDataList-method	fqName-methods
fqName<-	fqName-methods
fqName<-,FastqcData-method	fqName-methods
fqName<-,FastqcDataList-method	fqName-methods
gcAvail	gcAvail
gcAvail,TheoreticalGC-method	gcAvail
gcTheoretical	gcTheoretical
getColours	getColours-methods
getColours,PwfCols-method	getColours-methods
getGC	getGC
getGC,ANY-method	getGC
getGC,TheoreticalGC-method	getGC
getModule	getModule
getModule,ANY-method	getModule
getModule,FastpData-method	getModule
getModule,FastpDataList-method	getModule
getModule,FastqcData-method	getModule
getModule,FastqcDataList-method	getModule
getSummary	getSummary
getSummary,.FastqcFile-method	getSummary
getSummary,ANY-method	getSummary
getSummary,FastqcData-method	getSummary
getSummary,FastqcDataList-method	getSummary
importNgsLogs	importNgsLogs
importSJ	importSJ
isCompressed	isCompressed
maxAdapterContent	maxAdapterContent
mData	mData
mData,TheoreticalGC-method	mData
overRep2Fasta	overRep2Fasta-methods
overRep2Fasta,ANY-method	overRep2Fasta-methods
overRep2Fasta,FastqcData-method	overRep2Fasta-methods
overRep2Fasta,FastqcDataList-method	overRep2Fasta-methods
path	path
path,.FastpFile-method	path
path,.FastqcFile-method	path
path,FastpData-method	path
path,FastpDataList-method	path
path,FastqcData-method	path
path,FastqcDataList-method	path
plotAdapterContent	plotAdapterContent-methods
plotAdapterContent,ANY-method	plotAdapterContent-methods
plotAdapterContent,FastpData-method	plotAdapterContent-methods
plotAdapterContent,FastpDataList-method	plotAdapterContent-methods
plotAdapterContent,FastqcData-method	plotAdapterContent-methods
plotAdapterContent,FastqcDataList-method	plotAdapterContent-methods
plotAlignmentSummary	plotAlignmentSummary
plotAssemblyStats	plotAssemblyStats
plotBaseQuals	plotBaseQuals-methods
plotBaseQuals,ANY-method	plotBaseQuals-methods
plotBaseQuals,FastpData-method	plotBaseQuals-methods
plotBaseQuals,FastpDataList-method	plotBaseQuals-methods
plotBaseQuals,FastqcData-method	plotBaseQuals-methods
plotBaseQuals,FastqcDataList-method	plotBaseQuals-methods
plotDupLevels	plotDupLevels-methods
plotDupLevels,ANY-method	plotDupLevels-methods
plotDupLevels,FastpData-method	plotDupLevels-methods
plotDupLevels,FastpDataList-method	plotDupLevels-methods
plotDupLevels,FastqcData-method	plotDupLevels-methods
plotDupLevels,FastqcDataList-method	plotDupLevels-methods
plotFastqcPCA	plotFastqcPCA-methods
plotFastqcPCA,ANY-method	plotFastqcPCA-methods
plotFastqcPCA,character-method	plotFastqcPCA-methods
plotFastqcPCA,FastqcDataList-method	plotFastqcPCA-methods
plotGcContent	plotGcContent-methods
plotGcContent,ANY-method	plotGcContent-methods
plotGcContent,FastpData-method	plotGcContent-methods
plotGcContent,FastpDataList-method	plotGcContent-methods
plotGcContent,FastqcData-method	plotGcContent-methods
plotGcContent,FastqcDataList-method	plotGcContent-methods
plotInsertSize	plotInsertSize-methods
plotInsertSize,FastpData-method	plotInsertSize-methods
plotInsertSize,FastpDataList-method	plotInsertSize-methods
plotKmers	plotKmers-methods
plotKmers,ANY-method	plotKmers-methods
plotKmers,FastpData-method	plotKmers-methods
plotKmers,FastqcData-method	plotKmers-methods
plotKmers,FastqcDataList-method	plotKmers-methods
plotNContent	plotNContent-methods
plotNContent,ANY-method	plotNContent-methods
plotNContent,FastpData-method	plotNContent-methods
plotNContent,FastpDataList-method	plotNContent-methods
plotNContent,FastqcData-method	plotNContent-methods
plotNContent,FastqcDataList-method	plotNContent-methods
plotOverrep	plotOverrep-methods
plotOverrep,ANY-method	plotOverrep-methods
plotOverrep,character-method	plotOverrep-methods
plotOverrep,FastqcData-method	plotOverrep-methods
plotOverrep,FastqcDataList-method	plotOverrep-methods
plotReadTotals	plotReadTotals-methods
plotReadTotals,ANY-method	plotReadTotals-methods
plotReadTotals,FastpDataList-method	plotReadTotals-methods
plotReadTotals,FastqcDataList-method	plotReadTotals-methods
plotSeqContent	plotSeqContent-methods
plotSeqContent,ANY-method	plotSeqContent-methods
plotSeqContent,FastpData-method	plotSeqContent-methods
plotSeqContent,FastpDataList-method	plotSeqContent-methods
plotSeqContent,FastqcData-method	plotSeqContent-methods
plotSeqContent,FastqcDataList-method	plotSeqContent-methods
plotSeqLengthDistn	plotSeqLengthDistn-methods
plotSeqLengthDistn,ANY-method	plotSeqLengthDistn-methods
plotSeqLengthDistn,character-method	plotSeqLengthDistn-methods
plotSeqLengthDistn,FastqcData-method	plotSeqLengthDistn-methods
plotSeqLengthDistn,FastqcDataList-method	plotSeqLengthDistn-methods
plotSeqQuals	plotSeqQuals-methods
plotSeqQuals,ANY-method	plotSeqQuals-methods
plotSeqQuals,character-method	plotSeqQuals-methods
plotSeqQuals,FastqcData-method	plotSeqQuals-methods
plotSeqQuals,FastqcDataList-method	plotSeqQuals-methods
plotSummary	plotSummary-methods
plotSummary,ANY-method	plotSummary-methods
plotSummary,character-method	plotSummary-methods
plotSummary,FastqcDataList-method	plotSummary-methods
pwf	pwf
PwfCols	PwfCols-class
PwfCols-class	PwfCols-class
readTotals	readTotals
setAlpha	getColours-methods
setAlpha,PwfCols-method	getColours-methods
setColours	getColours-methods
setColours,PwfCols-method	getColours-methods
summariseOverrep	summariseOverrep-methods
summariseOverrep,FastpData-method	summariseOverrep-methods
summariseOverrep,FastpDataList-method	summariseOverrep-methods
summariseOverrep,FastqcData-method	summariseOverrep-methods
summariseOverrep,FastqcDataList-method	summariseOverrep-methods
TheoreticalGC-class	TheoreticalGC-class
writeHtmlReport	writeHtmlReport
[,FastpDataList,ANY,missing-method	extract-methods
[,FastpDataList,character,missing-method	extract-methods
[,FastpDataList,logical,missing-method	extract-methods
[,FastpDataList,numeric,missing-method	extract-methods
[,FastqcDataList,ANY,missing-method	extract-methods
[,FastqcDataList,character,missing-method	extract-methods
[,FastqcDataList,logical,missing-method	extract-methods
[,FastqcDataList,numeric,missing-method	extract-methods
