Files in RussBainer/gCrisprTools
Suite of Functions for Pooled Crispr Screen QC and Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/AlignmentBarchart.R
R/Crispr_Enrichment_test.R
R/DirTest.R
R/GCbias.R
R/GenePvalsFromEset.R
R/GeneratePRC.R
R/GenerateROC.R
R/GenerateSignalSummary.R
R/GuideCDF.R
R/Normalization.R
R/RRAalpha.R
R/RankByRep.R
R/Raw_read_densities.R
R/StackedGuides.R
R/ViewControls.R
R/ViewGuides.R
R/ViewTopTargets.R
R/annotations.R
R/compareContrasts.R
R/contrastScatter.R
R/discardTraceReads.R
R/fileutilities.R
R/gCrisprTools.R
R/generateCAT.R
R/generateReports.R
R/processFit.R
R/sparrow_integration.R
README.md
data/aln.RData
data/ann.RData
data/datalist
data/es.RData
data/essential.genes.RData
data/fit.RData
data/resultsDF.RData
inst/rmarkdown/templates/CRISPR_QC_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/CRISPR_QC_report/template.yaml
inst/rmarkdown/templates/CRISPR_contrast_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/CRISPR_contrast_report/template.yaml
inst/rmarkdown/templates/CRISPR_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/CRISPR_report/template.yaml
inst/unitTests/test.GenePvalsFromEset.R
inst/unitTests/test.RRAalpha.R
inst/unitTests/test.roc.R
man/aln.Rd
man/ann.Rd
man/appendDateAndExt.Rd
man/ct.CAT.Rd
man/ct.DirectionalTests.Rd
man/ct.GCbias.Rd
man/ct.GREATdb.Rd
man/ct.PRC.Rd
man/ct.ROC.Rd
man/ct.RRAaPvals.Rd
man/ct.RRAalpha.Rd
man/ct.RRAalphaBatch.Rd
man/ct.alignmentChart.Rd
man/ct.alphaBeta.Rd
man/ct.applyAlpha.Rd
man/ct.buildSE.Rd
man/ct.compareContrasts.Rd
man/ct.contrastBarchart.Rd
man/ct.drawColorLegend.Rd
man/ct.drawFlat.Rd
man/ct.ecdf.Rd
man/ct.expandAnnotation.Rd
man/ct.exprsColor.Rd
man/ct.filterReads.Rd
man/ct.gRNARankByReplicate.Rd
man/ct.generateResults.Rd
man/ct.guideCDF.Rd
man/ct.inputCheck.Rd
man/ct.keyCheck.Rd
man/ct.makeContrastReport.Rd
man/ct.makeQCReport.Rd
man/ct.makeReport.Rd
man/ct.makeRhoNull.Rd
man/ct.normalizeBySlope.Rd
man/ct.normalizeFQ.Rd
man/ct.normalizeGuides.Rd
man/ct.normalizeMedians.Rd
man/ct.normalizeNTC.Rd
man/ct.normalizeSpline.Rd
man/ct.numcores.Rd
man/ct.parseGeneSymbol.Rd
man/ct.prepareAnnotation.Rd
man/ct.preprocessFit.Rd
man/ct.rankSimple.Rd
man/ct.rawCountDensities.Rd
man/ct.regularizeContrasts.Rd
man/ct.resultCheck.Rd
man/ct.scatter.Rd
man/ct.seas.Rd
man/ct.seasPrep.Rd
man/ct.signalSummary.Rd
man/ct.simpleResult.Rd
man/ct.softLog.Rd
man/ct.stackGuides.Rd
man/ct.targetSetEnrichment.Rd
man/ct.topTargets.Rd
man/ct.upSet.Rd
man/ct.viewControls.Rd
man/ct.viewGuides.Rd
man/dir.writable.Rd
man/es.Rd
man/essential.genes.Rd
man/fit.Rd
man/gCrisprTools-package.Rd
man/initOutDir.Rd
man/renderReport.Rd
man/resultsDF.Rd
tests/unit.tests.R
vignettes/Contrast_Comparisons.Rmd
vignettes/Crispr_example_workflow.Rmd
vignettes/gCrisprTools_Vignette.Rmd
