Files in CrispRVariants

Tools for counting and visualising mutations in a target location

R/plotFreqHeatmap.R R/narrowAlignments.R R/alleleLabels.R R/mergeChimeras.R R/input_checks.R R/findChimeras.R R/seqsToAln.R R/initialisers.R R/CrisprRun.R R/crispRvariants_data.R R/accessors.R R/utils.R R/abifToFastq.R R/reverseCigar.R R/excludeFromBam.R R/plotChimeras.R R/refFromAlns.R R/barplotAlleleFreqs.R R/CrisprSet.R R/readsByPCRPrimer.R R/getInsertionsTable.R R/writeFastq.R R/plotVariants.R R/plotAlignments.R vignettes/user_guide.Rmd man/makeAlignmentTilePlot.Rd man/barplotAlleleFreqs.Rd man/variantCounts.Rd man/addCodonFrame.Rd man/plotFreqHeatmap.Rd man/plotVariants.Rd man/intersperse.Rd man/dispatchDots.Rd man/setDNATileColours.Rd man/collapsePairs.Rd man/addClipped.Rd man/alleles.Rd man/plotAlignments.Rd man/getInsertionsTable.Rd man/CrisprRun-class.Rd man/transformAlnsToLong.Rd man/findSNVs.Rd man/reverseCigar.Rd man/excludeFromBam.Rd man/selectAlnRegionsHelpers.Rd man/arrangePlots.Rd man/consensusSeqs.Rd man/narrowAlignments.Rd man/mergeCrisprSets.Rd man/mutationEfficiency.Rd man/selectOps.Rd man/findChimeras.Rd man/mismatchLabels.Rd man/readsToTarget.Rd man/readTargetBam.Rd man/getChimeras.Rd man/rcAlns.Rd man/annotateGenePlot.Rd man/writeFastq.Rd man/CrisprSet-class.Rd man/readsByPCRPrimer.Rd man/abifToFastq.Rd man/setMismatchTileColours.Rd man/indelLabels.Rd man/refFromAlns.Rd man/mergeChimeras.Rd man/rmMultiPCRChimera.Rd man/indelCounts.Rd man/explodeCigarOpCombs.Rd man/getAxisCoords.Rd man/gol_clutch1.Rd man/alns.Rd man/seqsToAln.Rd man/plotChimeras.Rd man/alleleLabelsHelpers.Rd tests/testthat.R tests/testthat/test-narrowAlignments.R tests/testthat/test-seqsToAln.R tests/testthat/test-refsToAln.R tests/testthat/test-initialisers.R tests/testthat/test-accessors.R tests/testthat/test-utils.R tests/testthat/test-plotAlignments.R tests/testthat/test-annotate-plot.R inst/doc/user_guide.R inst/doc/user_guide.pdf inst/doc/user_guide.Rmd