Files in ngsReports

Load FastqQC reports and other NGS related files

README.md tests/testthat.R tests/testthat/test-getSummary.R tests/testthat/test-getTheoreticalGC.R tests/testthat/test-fqName.R tests/testthat/test-addPercent.R tests/testthat/test-validTemplate.R tests/testthat/test-NullHandling.R tests/testthat/test-FastqcFile.R tests/testthat/test-maxAdapterContent.R tests/testthat/test-fqcVersion.R tests/testthat/test-getModuleErrNulls.R tests/testthat/test-runFastQC.R tests/testthat/test-importLogs.R tests/testthat/test-getModuleFunctions.R tests/testthat/test-importSJ.R tests/testthat/test-Subsetting.R tests/testthat/test-makeDendrogram.R tests/testthat/test-renderDendro.R tests/testthat/test-emptyPlot.R tests/testthat/test-plotFastqcPCA.R tests/testthat/test-moduleMessages.R tests/testthat/test-makeLabels.R tests/testthat/test-makeSidebar.R tests/testthat/test-splitByTab.R tests/testthat/test-isCompressed.R tests/testthat/test-PwfCols.R R/FastqcFile.R R/fqName.R R/writeHtmlReport.R R/plotSummary.R R/PwfCols.R R/getSummary.R R/plotSeqLengthDistn.R R/plotSeqContent.R R/validationFunctions.R R/plotDupLevels.R R/overRep2Fasta.R R/plotNContent.R R/fqcVersion.R R/plotReadTotals.R R/isCompressed.R R/ngsReports-package.R R/extract.R R/importNgsLogs.R R/maxAdapterContent.R R/plotKmers.R R/plotAlignmentSummary.R R/FastqcData.R R/helpers.R R/S4coercion.R R/plotAdapterContent.R R/AllGenerics.R R/readTotals.R R/plotSeqQuals.R R/plotAssemblyStats.R R/getColours.R R/estGcDistn.R R/aaa.R R/plotOverrep.R R/getGC.R R/plotGcContent.R R/pwf.R R/data.R R/getModule.R R/plotFastqcPCA.R R/importSJ.R R/plotBaseQuals.R R/FastqcDataList.R R/runFastQC.R R/path.R R/errMsg.R R/TheoreticalGC.R man/extract-methods.Rd man/pwf.Rd man/dot-getToolName.Rd man/plotOverrep-methods.Rd man/isCompressed.Rd man/dot-isValidDuplicationMetricsLog.Rd man/gcTheoretical.Rd man/FastqcDataList.Rd man/runFastQC-methods.Rd man/dot-parseStarLogs.Rd man/maxAdapterContent.Rd man/dot-scale_fill_pwf.Rd man/plotDupLevels-methods.Rd man/plotSeqQuals-methods.Rd man/plotKmers-methods.Rd man/dot-parseBowtieLogs.Rd man/dot-isValidFlagstatLog.Rd man/dot-makeSidebar.Rd man/dot-isValidFeatureCountsLog.Rd man/dot-parseBuscoLogs.Rd man/dot-parseCutadaptLogs.Rd man/getGC.Rd man/getColours-methods.Rd man/plotReadTotals-methods.Rd man/plotSummary-methods.Rd man/plotNContent-methods.Rd man/dot-hidePWFRects.Rd man/dot-isValidQuastLog.Rd man/dot-isValidCutadaptLog.Rd man/dot-parseDuplicationMetricsLogs.Rd man/dot-renderDendro.Rd man/dot-makeDendro.Rd man/dot-parseFlagstatLogs.Rd man/dot-isValidBowtieLog.Rd man/dot-parseAdapterRemovalLogs.Rd man/dot-isValidBuscoLog.Rd man/writeHtmlReport.Rd man/estGcDistn.Rd man/getModule.Rd man/dot-parseHisat2Logs.Rd man/dot-parseFeatureCountsLogs.Rd man/mData.Rd man/dot-addPercent.Rd man/overRep2Fasta-methods.Rd man/readTotals.Rd man/dot-isValidHisat2Log.Rd man/path.Rd man/PwfCols-class.Rd man/dot-splitByTab.Rd man/dot-isValidStarLog.Rd man/plotBaseQuals-methods.Rd man/fqcVersion.Rd man/importSJ.Rd man/FastqcData.Rd man/TheoreticalGC-class.Rd man/plotAssemblyStats.Rd man/gcAvail.Rd man/dot-FastqcFile-class.Rd man/dot-isValidTrimmomaticLog.Rd man/plotSeqContent-methods.Rd man/plotGcContent-methods.Rd man/plotFastqcPCA-methods.Rd man/plotAdapterContent-methods.Rd man/fqName-methods.Rd man/getSummary.Rd man/dot-makeLabels.Rd man/dot-isValidAdapterRemovalLog.Rd man/importNgsLogs.Rd man/dot-emptyPlot.Rd man/dot-parseQuastLogs.Rd man/plotAlignmentSummary.Rd man/dot-parseTrimmomaticLogs.Rd man/plotSeqLengthDistn-methods.Rd inst/extdata/ngsReports_Fastqc.Rmd inst/doc/ngsReportsIntroduction.Rmd inst/doc/ngsReportsIntroduction.R build/ngsReports.pdf vignettes/ngsReportsIntroduction.Rmd