Files in ThomasCarroll/basecallQC
Working with Illumina Basecalling and Demultiplexing input and output files
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/FastQCShortRead_Functions.R
R/allClasses.R
R/allMethods.R
R/plots.R
R/processExternalFormats_Functions.R
R/processIlluminaSamplesheets_Functions.R
R/processInterOps_Functions.R
R/processXMLs_Functions.R
R/reporting.R
R/tables.R
README.md
basecallQC.Rproj
inst/NEWS.Rd
inst/extdata/AdapterTrimming.txt
inst/extdata/ConversionStats.xml
inst/extdata/DemultiplexingStats.xml
inst/extdata/DemuxSummaryF1L1.txt
inst/extdata/FastqSummaryF1L1.txt
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX.csv
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/Stats/AdapterTrimming.txt
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/Stats/ConversionStats.xml
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/Stats/DemultiplexingStats.xml
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/Stats/DemuxSummaryF1L1.txt
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/Stats/FastqSummaryF1L1.txt
inst/extdata/Runs/161105_D00467_0205_AC9L0AANXX/runParameters.xml
inst/extdata/Runs/170217_D00467_0227_ACADN3ANXX/CADN3ANXX.csv
inst/extdata/Runs/170217_D00467_0227_ACADN3ANXX/runParameters.xml
inst/extdata/Runs/170222_D00467_0228_ACAL6PANXX/CAL6PANXX.csv
inst/extdata/Runs/170222_D00467_0228_ACAL6PANXX/runParameters.xml
inst/extdata/Runs/170303_D00467_0230_BCA7RDANXX/CAL7DANXX.csv
inst/extdata/Runs/170303_D00467_0230_BCA7RDANXX/runParameters.xml
inst/extdata/Runs/170303_D00467_0231_ACAK02ANXX/CAK02ANXX.csv
inst/extdata/Runs/170303_D00467_0231_ACAK02ANXX/runParameters.xml
inst/extdata/config.ini
inst/extdata/reportRMDs/basecallqcreport.Rmd
inst/extdata/runParameters.xml
inst/extdata/testSS.csv
inst/extdata/testSampleSheets/ErroneousNewSamplesheet.csv
inst/extdata/testSampleSheets/OldSamplesheet.csv
inst/extdata/testSampleSheets/runParameters.xml
man/BCL2FastQparams.Rd
man/baseCallMetrics.Rd
man/basecallQC.Rd
man/createBCLcommand.Rd
man/createBasemasks.Rd
man/demultiplexMetrics.Rd
man/demuxBarplot.Rd
man/demuxBoxplot.Rd
man/indexlengths.Rd
man/interOpsReport.Rd
man/makeFQTable.Rd
man/passFilterBar.Rd
man/passFilterBoxplot.Rd
man/passFilterTileplot.Rd
man/readlengths.Rd
man/reportBCL.Rd
man/summaryConvStatsTable.Rd
man/summaryDemuxTable.Rd
man/validateBCLSheet.Rd
tests/testthat.R
tests/testthat/C9L0AANXX.csv
tests/testthat/CA7RDANXX.csv
tests/testthat/CADN3ANXX.csv
tests/testthat/CAK02ANXX.csv
tests/testthat/CAL6PANXX.csv
tests/testthat/test_Run1.R
tests/testthat/test_Run2.R
tests/testthat/test_Run3.R
tests/testthat/test_Run4.R
tests/testthat/test_Run5.R
vignettes/C7JE1ANXX.csv
vignettes/basecallQC.Rmd
vignettes/imgs/inputDir.jpg
vignettes/imgs/outputDir.jpg
