UofABioinformaticsHub/fastqcReports
Load FastqQC reports and other NGS related files

Package index
Search the UofABioinformaticsHub/fastqcReports package
Vignettes
Functions
285
Source code
88
Man pages
73
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UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files
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API

API for UofABioinformaticsHub/fastqcReports
Load FastqQC reports and other NGS related files

Global functions
.FastpFile Source code
.FastpFile-class Man page
.FastqcFile Source code
.FastqcFile-class Man page
.addPercent Man page Source code
.emptyPlot Man page Source code
.errNotImp Source code
.generatePer_base_sequence_contentPCA Source code
.generatePer_base_sequence_qualityPCA Source code
.generatePer_sequence_GC_contentPCA Source code
.generatePer_sequence_quality_scoresPCA Source code
.generateSequence_Length_DistributionPCA Source code
.getAdapterCont Source code
.getBasicStatistics Source code
.getFpAdapters Source code
.getFpBeforeAfter Source code
.getFpDuplication Source code
.getFpInsert Source code
.getFpSummary Source code
.getFqcLines Source code
.getKmerCont Source code
.getOverrepSeq Source code
.getPerBaseNCont Source code
.getPerBaseSeqCont Source code
.getPerBaseSeqQuals Source code
.getPerSeqGcCont Source code
.getPerSeqQualScores Source code
.getPerTileSeqQuals Source code
.getSeqDuplicationLevels Source code
.getSeqLengthDist Source code
.getToolName Man page Source code
.hidePWFRects Man page Source code
.initialiseOutput Source code
.isValidAdapterRemovalLog Source code
.isValidBowtieLog Source code
.isValidBuscoLog Source code
.isValidCutadaptLog Source code
.isValidDuplicationMetricsLog Source code
.isValidFastpData Source code
.isValidFastpDataList Source code
.isValidFastpFile Source code
.isValidFastqcData Source code
.isValidFastqcDataList Source code
.isValidFastqcFile Source code
.isValidFeatureCountsLog Source code
.isValidFlagstatLog Source code
.isValidHisat2Log Source code
.isValidMacs2CallpeakLog Source code
.isValidPwf Source code
.isValidQuastLog Source code
.isValidRnaseqcMetricsLog Source code
.isValidSJ Source code
.isValidSalmonLibFormatCountsLog Source code
.isValidSalmonMetaInfoLog Source code
.isValidStarLog Source code
.isValidTheoreticalGC Source code
.isValidTrimmomaticLog Source code
.isValidUmitoolsDedupLog Source code
.makeDendro Man page Source code
.makeLabels Man page Source code
.makePwfGradient Man page Source code
.makeSidebar Man page Source code
.parseAdapterRemovalLogs Man page Source code
.parseBowtieLogs Man page Source code
.parseBuscoLogs Man page Source code
.parseCutadaptLogs Man page Source code
.parseDuplicationMetricsLogs Man page Source code
.parseFeatureCountsLogs Man page Source code
.parseFlagstatLogs Man page Source code
.parseHisat2Logs Man page Source code
.parseMacs2CallpeakLogs Man page Source code
.parseQuastLogs Man page Source code
.parseRnaseqcMetricsLogs Man page Source code
.parseSalmonLibFormatCountsLogs Man page Source code
.parseSalmonMetaInfoLogs Man page Source code
.parseStarLogs Man page Source code
.parseTrimmomaticLogs Man page Source code
.parseUmitoolsDedupLogs Man page Source code
.plotBowtieAlignment Source code
.plotBuscoStats Source code
.plotHisat2Alignment Source code
.plotQuastStats Source code
.plotStarAlignment Source code
.prepHeatmap Man page Source code
.renderDendro Man page Source code
.splitByTab Man page Source code
.tidyAc Source code
.updateThemeFromDots Man page Source code
FastpData Man page Source code
FastpData-class Man page
FastpDataList Man page Source code
FastpDataList-class Man page
FastqcData Man page Source code
FastqcData-class Man page
FastqcDataList Man page Source code
FastqcDataList-class Man page
PwfCols Man page
PwfCols-class Man page
TheoreticalGC-class Man page
[,FastpDataList,ANY,missing-method Man page
[,FastpDataList,character,missing-method Man page
[,FastpDataList,logical,missing-method Man page
[,FastpDataList,numeric,missing-method Man page
[,FastqcDataList,ANY,missing-method Man page
[,FastqcDataList,character,missing-method Man page
[,FastqcDataList,logical,missing-method Man page
[,FastqcDataList,numeric,missing-method Man page
estGcDistn Man page
estGcDistn,ANY-method Man page
estGcDistn,DNAStringSet-method Man page
estGcDistn,character-method Man page
fqName Man page
fqName,ANY-method Man page
fqName,FastpData-method Man page
fqName,FastpDataList-method Man page
fqName,FastqcData-method Man page
fqName,FastqcDataList-method Man page
fqName<- Man page
fqName<-,FastqcData-method Man page
fqName<-,FastqcDataList-method Man page
fqcVersion Man page
fqcVersion,ANY-method Man page
fqcVersion,FastqcData-method Man page
fqcVersion,FastqcDataList-method Man page
gcAvail Man page
gcAvail,TheoreticalGC-method Man page
gcTheoretical Man page
getColours Man page
getColours,PwfCols-method Man page
getGC Man page
getGC,ANY-method Man page
getGC,TheoreticalGC-method Man page
getModule Man page
getModule,ANY-method Man page
getModule,FastpData-method Man page
getModule,FastpDataList-method Man page
getModule,FastqcData-method Man page
getModule,FastqcDataList-method Man page
getSummary Man page
getSummary,.FastqcFile-method Man page
getSummary,ANY-method Man page
getSummary,FastqcData-method Man page
getSummary,FastqcDataList-method Man page
importNgsLogs Man page Source code
importSJ Man page Source code
isCompressed Man page Source code
mData Man page
mData,TheoreticalGC-method Man page
maxAdapterContent Man page Source code
overRep2Fasta Man page
overRep2Fasta,ANY-method Man page
overRep2Fasta,FastqcData-method Man page
overRep2Fasta,FastqcDataList-method Man page
path Man page
path,.FastpFile-method Man page
path,.FastqcFile-method Man page
path,FastpData-method Man page
path,FastpDataList-method Man page
path,FastqcData-method Man page
path,FastqcDataList-method Man page
plotAdapterContent Man page
plotAdapterContent,ANY-method Man page
plotAdapterContent,FastpData-method Man page
plotAdapterContent,FastpDataList-method Man page
plotAdapterContent,FastqcData-method Man page
plotAdapterContent,FastqcDataList-method Man page
plotAlignmentSummary Man page Source code
plotAssemblyStats Man page Source code
plotBaseQuals Man page
plotBaseQuals,ANY-method Man page
plotBaseQuals,FastpData-method Man page
plotBaseQuals,FastpDataList-method Man page
plotBaseQuals,FastqcData-method Man page
plotBaseQuals,FastqcDataList-method Man page
plotDupLevels Man page
plotDupLevels,ANY-method Man page
plotDupLevels,FastpData-method Man page
plotDupLevels,FastpDataList-method Man page
plotDupLevels,FastqcData-method Man page
plotDupLevels,FastqcDataList-method Man page
plotFastqcPCA Man page
plotFastqcPCA,ANY-method Man page
plotFastqcPCA,FastqcDataList-method Man page
plotFastqcPCA,character-method Man page
plotGcContent Man page
plotGcContent,ANY-method Man page
plotGcContent,FastpData-method Man page
plotGcContent,FastpDataList-method Man page
plotGcContent,FastqcData-method Man page
plotGcContent,FastqcDataList-method Man page
plotInsertSize Man page
plotInsertSize,FastpData-method Man page
plotInsertSize,FastpDataList-method Man page
plotKmers Man page
plotKmers,ANY-method Man page
plotKmers,FastpData-method Man page
plotKmers,FastqcData-method Man page
plotKmers,FastqcDataList-method Man page
plotNContent Man page
plotNContent,ANY-method Man page
plotNContent,FastpData-method Man page
plotNContent,FastpDataList-method Man page
plotNContent,FastqcData-method Man page
plotNContent,FastqcDataList-method Man page
plotOverrep Man page
plotOverrep,ANY-method Man page
plotOverrep,FastqcData-method Man page
plotOverrep,FastqcDataList-method Man page
plotOverrep,character-method Man page
plotReadTotals Man page
plotReadTotals,ANY-method Man page
plotReadTotals,FastpDataList-method Man page
plotReadTotals,FastqcDataList-method Man page
plotSeqContent Man page
plotSeqContent,ANY-method Man page
plotSeqContent,FastpData-method Man page
plotSeqContent,FastpDataList-method Man page
plotSeqContent,FastqcData-method Man page
plotSeqContent,FastqcDataList-method Man page
plotSeqLengthDistn Man page
plotSeqLengthDistn,ANY-method Man page
plotSeqLengthDistn,FastqcData-method Man page
plotSeqLengthDistn,FastqcDataList-method Man page
plotSeqLengthDistn,character-method Man page
plotSeqQuals Man page
plotSeqQuals,ANY-method Man page
plotSeqQuals,FastqcData-method Man page
plotSeqQuals,FastqcDataList-method Man page
plotSeqQuals,character-method Man page
plotSummary Man page
plotSummary,ANY-method Man page
plotSummary,FastqcDataList-method Man page
plotSummary,character-method Man page
pwf Man page
readTotals Man page Source code
setAlpha Man page
setAlpha,PwfCols-method Man page
setColours Man page
setColours,PwfCols-method Man page
summariseOverrep Man page
summariseOverrep,FastpData-method Man page
summariseOverrep,FastpDataList-method Man page
summariseOverrep,FastqcData-method Man page
summariseOverrep,FastqcDataList-method Man page
writeHtmlReport Man page Source code
UofABioinformaticsHub/fastqcReports documentation built on April 1, 2024, 5:29 p.m.

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