Files in steveped/ngsReports

Load FastqQC reports and other NGS related files

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/AllGenerics.R R/FastpData.R R/FastpDataList.R R/FastpFile.R R/FastqcData.R R/FastqcDataList.R R/FastqcFile.R R/PwfCols.R R/S4coercion.R R/TheoreticalGC.R R/aaa.R R/data.R R/errMsg.R R/estGcDistn.R R/extract.R R/fqName.R R/fqcVersion.R R/getColours.R R/getGC.R R/getModule.R R/getSummary.R R/helpers.R R/importNgsLogs.R R/importSJ.R R/isCompressed.R R/maxAdapterContent.R R/ngsReports-package.R R/overRep2Fasta.R R/path.R R/plotAdapterContent.R R/plotAlignmentSummary.R R/plotAssemblyStats.R R/plotBaseQuals.R R/plotDupLevels.R R/plotFastqcPCA.R R/plotGcContent.R R/plotInsertSize.R R/plotKmers.R R/plotNContent.R R/plotOverrep.R R/plotReadTotals.R R/plotSeqContent.R R/plotSeqLengthDistn.R R/plotSeqQuals.R R/plotSummary.R R/pwf.R R/readTotals.R R/summariseOverrep.R R/validationFunctions.R R/writeHtmlReport.R README.md TODO.md

data/gcTheoretical.RData

inst/CITATION

inst/NEWS

inst/extdata/ATTG_R1_fastqc.zip

inst/extdata/ATTG_R2_fastqc.zip

inst/extdata/Athaliana.TAIR10.tRNA.fasta.gz

inst/extdata/CCGC_R1_fastqc.zip

inst/extdata/CCGC_R2_fastqc.zip

inst/extdata/GACC_R1_fastqc.zip

inst/extdata/GACC_R2_fastqc.zip

inst/extdata/SJ.out.tab

inst/extdata/Sample1.trimmomaticPE.txt

inst/extdata/Sample1_Dedup_metrics.txt

inst/extdata/Sample2.trimmomaticSE.txt

inst/extdata/adapterRemoval.settings

inst/extdata/bowtie2PE.txt

inst/extdata/bowtie2SE.txt

inst/extdata/bowtiePE.txt

inst/extdata/bowtieSE.txt

inst/extdata/chr1.bam.metrics.tsv.gz

inst/extdata/cutadapt_full.txt

inst/extdata/cutadapt_minimal.txt

inst/extdata/errorTestingFiles/completelyEmpty.zip

inst/extdata/errorTestingFiles/hello.txt.gz

inst/extdata/errorTestingFiles/moduleNamesNoData.zip

inst/extdata/exampleRNASeq_R1_fastqc/fastqc_data.txt

inst/extdata/exampleRNASeq_R1_fastqc/summary.txt

inst/extdata/exampleRNASeq_R2_fastqc/fastqc_data.txt

inst/extdata/exampleRNASeq_R2_fastqc/summary.txt

inst/extdata/fastp.json.gz

inst/extdata/featureCounts.summary

inst/extdata/flagstat.txt

inst/extdata/hisat2PE.txt

inst/extdata/log.final.out

inst/extdata/macs2_callpeak.txt

inst/extdata/ngsReports_Fastqc.Rmd

inst/extdata/quast1.tsv

inst/extdata/quast2.tsv

inst/extdata/short_summary_Dmelanogaster_Busco.txt

inst/extdata/umitoolsDedup.txt

man/FastpData.Rd man/FastpDataList.Rd man/FastqcData.Rd man/FastqcDataList.Rd man/PwfCols-class.Rd man/TheoreticalGC-class.Rd man/dot-FastpFile-class.Rd man/dot-FastqcFile-class.Rd man/dot-addPercent.Rd man/dot-emptyPlot.Rd man/dot-getToolName.Rd man/dot-hidePWFRects.Rd man/dot-makeDendro.Rd man/dot-makeLabels.Rd man/dot-makePwfGradient.Rd man/dot-makeSidebar.Rd man/dot-parseAdapterRemovalLogs.Rd man/dot-parseBowtieLogs.Rd man/dot-parseBuscoLogs.Rd man/dot-parseCutadaptLogs.Rd man/dot-parseDuplicationMetricsLogs.Rd man/dot-parseFeatureCountsLogs.Rd man/dot-parseFlagstatLogs.Rd man/dot-parseHisat2Logs.Rd man/dot-parseMacs2CallpeakLogs.Rd man/dot-parseQuastLogs.Rd man/dot-parseRnaseqcMetricsLogs.Rd man/dot-parseSalmonLibFormatCountsLogs.Rd man/dot-parseSalmonMetaInfoLogs.Rd man/dot-parseStarLogs.Rd man/dot-parseTrimmomaticLogs.Rd man/dot-parseUmitoolsDedupLogs.Rd man/dot-prepHeatmap.Rd man/dot-renderDendro.Rd man/dot-splitByTab.Rd man/dot-updateThemeFromDots.Rd man/estGcDistn.Rd man/extract-methods.Rd

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man/figures/lifecycle-experimental.svg

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man/figures/ngsReports.png

man/fqName-methods.Rd man/fqcVersion.Rd man/gcAvail.Rd man/gcTheoretical.Rd man/getColours-methods.Rd man/getGC.Rd man/getModule.Rd man/getSummary.Rd man/importNgsLogs.Rd man/importSJ.Rd man/isCompressed.Rd man/mData.Rd man/maxAdapterContent.Rd man/overRep2Fasta-methods.Rd man/path.Rd man/plotAdapterContent-methods.Rd man/plotAlignmentSummary.Rd man/plotAssemblyStats.Rd man/plotBaseQuals-methods.Rd man/plotDupLevels-methods.Rd man/plotFastqcPCA-methods.Rd man/plotGcContent-methods.Rd man/plotInsertSize-methods.Rd man/plotKmers-methods.Rd man/plotNContent-methods.Rd man/plotOverrep-methods.Rd man/plotReadTotals-methods.Rd man/plotSeqContent-methods.Rd man/plotSeqLengthDistn-methods.Rd man/plotSeqQuals-methods.Rd man/plotSummary-methods.Rd man/pwf.Rd man/readTotals.Rd man/summariseOverrep-methods.Rd man/writeHtmlReport.Rd tests/testthat.R tests/testthat/setup.R tests/testthat/test-FastpFile.R tests/testthat/test-FastqcFile.R tests/testthat/test-NullHandling.R tests/testthat/test-PwfCols.R tests/testthat/test-Subsetting.R tests/testthat/test-addPercent.R tests/testthat/test-allPlots.R tests/testthat/test-emptyPlot.R tests/testthat/test-fqName.R tests/testthat/test-fqcVersion.R tests/testthat/test-getModuleErrNulls.R tests/testthat/test-getModuleFunctions.R tests/testthat/test-getSummary.R tests/testthat/test-getTheoreticalGC.R tests/testthat/test-importLogs.R tests/testthat/test-importSJ.R tests/testthat/test-isCompressed.R tests/testthat/test-makeDendrogram.R tests/testthat/test-makeLabels.R tests/testthat/test-makeSidebar.R tests/testthat/test-maxAdapterContent.R tests/testthat/test-moduleMessages.R tests/testthat/test-plotAdapterContent.R tests/testthat/test-plotBaseQuals.R tests/testthat/test-plotDupLevels.R tests/testthat/test-plotGcContent.R tests/testthat/test-plotInsertSize.R tests/testthat/test-plotKmers.R tests/testthat/test-plotNContent.R tests/testthat/test-plotReadTotals.R tests/testthat/test-plotSeqContent.R tests/testthat/test-prepHeatmap.R tests/testthat/test-renderDendro.R tests/testthat/test-splitByTab.R tests/testthat/test-summariseOverrep.R tests/testthat/test-validTemplate.R vignettes/ngsReportsIntroduction.Rmd

steveped/ngsReports documentation built on April 2, 2024, 5:10 p.m.