Files in jweile/tileseqMave

TileSeq MAVE Analysis pipeline

LICENSE.md R/buildJointTable.R R/csvParam2Json.R R/dropoutAnalysis.R R/enrichment.R R/fluorScore.R R/fluorSim.R R/joinRawInputs.R R/legacy.R R/libraryQC.R R/logging.R R/mavedbCountExport.R R/parseCountFile.R R/runAlignments.R R/scaling.R R/selectionQC.R R/simulate.R R/startup.R README.md README.pdf inst/scripts/calcEnrichment.R inst/scripts/calcLLR.R inst/scripts/calibratePhred.R inst/scripts/collapseSamples.R inst/scripts/colorizeStructure.R inst/scripts/condenseQC.R inst/scripts/csv2json.R inst/scripts/differenceMap.R inst/scripts/drawPRC.R inst/scripts/dropoutTS.R inst/scripts/exportCounts.R inst/scripts/joinCounts.R inst/scripts/legacy/contamination.R inst/scripts/legacy/convertForJoe.R inst/scripts/legacy/processDatasets.R inst/scripts/legacy/refine.R inst/scripts/legacy/translateCounts.R inst/scripts/linkBinaries.R inst/scripts/mavevisLocal.R inst/scripts/mergeMaps.R inst/scripts/popcodeOligos.R inst/scripts/prcNormalize.R inst/scripts/profileWTCtrl.R inst/scripts/proveanInput.R inst/scripts/proveanNormalize.R inst/scripts/referenceSets.R inst/scripts/runLibraryQC.R inst/scripts/runSelectionQC.R inst/scripts/scaleScores.R inst/scripts/selfupdate.R man/adhocLogPhiSD.Rd man/adjustTableDepth.Rd man/analyzeComplexity.Rd man/analyzeLegacyTileseqCounts.Rd man/biasCorrection.Rd man/bnl.Rd man/buildJointTable.Rd man/buildPlotMatrix.Rd man/buildSimplifiedMarginal.Rd man/calcDepthDrops.Rd man/calcEnrichment.Rd man/calcPhi.Rd man/calculateFits.Rd man/charProfile.Rd man/checkCSV.Rd man/codonAgreement.Rd man/collapseByAA.Rd man/countAttributes.Rd man/coverageSubmap.Rd man/csvParam2Json.Rd man/dot-onAttach.Rd man/drawComplexity.Rd man/drawCoverageLegend.Rd man/drawCoverageMap.Rd man/drawDistributions.Rd man/drawNucleotideBias.Rd man/drawPositionalDepth.Rd man/dropoutAnalysis.Rd man/enactScale.Rd man/errorProfile.Rd man/expectedError.Rd man/exportExperiment.Rd man/exportRawAssay.Rd man/exportSeqSample.Rd man/filterProgression.Rd man/filterVariants.Rd man/findQuads.Rd man/findRuns.Rd man/fit.cv.model.Rd man/floor0.Rd man/flooring.Rd man/fluorScore.Rd man/getNonselectFor.Rd man/getNonselects.Rd man/getNsConditions.Rd man/getPivotOverrides.Rd man/getSelects.Rd man/getTimepointsFor.Rd man/getWTControlFor.Rd man/getWTReps.Rd man/inferTiles.Rd man/join.datapoints.Rd man/joinRawInputs.Rd man/latestSubDir.Rd man/legacyCountConverter.Rd man/libraryQC.Rd man/libraryQCLegacy.Rd man/log.sd.Rd man/logInfo.Rd man/logPhiBias.Rd man/logVersion.Rd man/logWarn.Rd man/mavedbCountExport.Rd man/mean.sd.count.Rd man/mut_breakdown.Rd man/nucleotideBiasAnalysis.Rd man/parseCountFile.Rd man/parseCoverageFile.Rd man/parseParameters.Rd man/pdftagger.Rd man/plotCensus.Rd man/plotCoverageCurve.Rd man/plotDepthDrops.Rd man/plotFrameshiftHotspot.Rd man/plotJackpotDiagnosis.Rd man/plotMutbreakdown.Rd man/plotReplicateCorrelation.Rd man/plotSeqErrorRates.Rd man/plotWTCtrl.Rd man/ratio.sd.Rd man/rawFilter.Rd man/reachableChanges.Rd man/regionCensus.Rd man/registerLogger.Rd man/regularizationQC.Rd man/regularizeRaw.Rd man/replicateCorrelation.Rd man/residualError.Rd man/runModelFits.Rd man/scaleScores.Rd man/scoreDistributions.Rd man/selectionQC.Rd man/simulateAssay.Rd man/simulateExperiment.Rd man/simulateFitness.Rd man/simulatePool.Rd man/simulateTileSeq.Rd man/slide.Rd man/splitCodonChanges.Rd man/startupMessage.Rd man/synNonDelta.Rd man/tileCensus.Rd man/tilesInRegions.Rd man/validateParameters.Rd tests/testthat.R tests/testthat/testCsv2Json.R tests/testthat/testTranslateHGVS.R