Files in HLindsay/CrispRVariants
Tools for counting and visualising mutations in a target location
.Rbuildignore
.travis.yml
DESCRIPTION
NAMESPACE
R/CrisprRun.R
R/CrisprSet.R
R/abifToFastq.R
R/accessors.R
R/alleleLabels.R
R/barplotAlleleFreqs.R
R/crispRvariants_data.R
R/excludeFromBam.R
R/findChimeras.R
R/getInsertionsTable.R
R/initialisers.R
R/input_checks.R
R/mergeChimeras.R
R/narrowAlignments.R
R/plotAlignments.R
R/plotChimeras.R
R/plotFreqHeatmap.R
R/plotVariants.R
R/readsByPCRPrimer.R
R/refFromAlns.R
R/reverseCigar.R
R/seqsToAln.R
R/utils.R
R/writeFastq.R
data/gol_clutch1.rda
inst/CITATION
inst/NEWS.Rd
inst/doc/user_guide.R
inst/doc/user_guide.Rmd
inst/doc/user_guide.pdf
inst/extdata/Danio_rerio.Zv9.73.gol.sqlite
inst/extdata/GRCz10_81_ptena_txdb.sqlite
inst/extdata/IM2033.ab1
inst/extdata/ab1/ptena/phenotype/embryo1/AB2001.ab1
inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam
inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam.bai
inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam
inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam.bai
inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam
inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam.bai
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam.bai
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam
inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam.bai
inst/extdata/bed/guide.bed
inst/extdata/cntnap2b_test_data.fastq.gz
inst/extdata/cntnap2b_test_data_guide.bed
inst/extdata/cntnap2b_test_data_s.bam
inst/extdata/gol_F1_clutch_1_embryo_1_s.bam
inst/extdata/gol_F1_clutch_1_embryo_1_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_2_s.bam
inst/extdata/gol_F1_clutch_1_embryo_2_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_3_s.bam
inst/extdata/gol_F1_clutch_1_embryo_3_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_4_s.bam
inst/extdata/gol_F1_clutch_1_embryo_4_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_5_s.bam
inst/extdata/gol_F1_clutch_1_embryo_5_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_6_s.bam
inst/extdata/gol_F1_clutch_1_embryo_6_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_7_s.bam
inst/extdata/gol_F1_clutch_1_embryo_7_s.bam.bai
inst/extdata/gol_F1_clutch_1_embryo_8_s.bam
inst/extdata/gol_F1_clutch_1_embryo_8_s.bam.bai
inst/extdata/gol_F1_clutch_2_embryo_4_s.bam
inst/extdata/gol_F1_clutch_2_embryo_4_s.bam.bai
inst/extdata/gol_F1_metadata.txt
inst/extdata/gol_F1_metadata_small.txt
inst/extdata/metadata/metadata.xls
inst/extdata/ptena_GRCHz10_ref.rda
inst/extdata/wtx_Sanger.png
man/CrisprRun-class.Rd
man/CrisprSet-class.Rd
man/abifToFastq.Rd
man/addClipped.Rd
man/addCodonFrame.Rd
man/alleleLabelsHelpers.Rd
man/alleles.Rd
man/alns.Rd
man/annotateGenePlot.Rd
man/arrangePlots.Rd
man/barplotAlleleFreqs.Rd
man/collapsePairs.Rd
man/consensusSeqs.Rd
man/dispatchDots.Rd
man/excludeFromBam.Rd
man/explodeCigarOpCombs.Rd
man/findChimeras.Rd
man/findSNVs.Rd
man/getAxisCoords.Rd
man/getChimeras.Rd
man/getInsertionsTable.Rd
man/gol_clutch1.Rd
man/indelCounts.Rd
man/indelLabels.Rd
man/intersperse.Rd
man/makeAlignmentTilePlot.Rd
man/mergeChimeras.Rd
man/mergeCrisprSets.Rd
man/mismatchLabels.Rd
man/mutationEfficiency.Rd
man/narrowAlignments.Rd
man/plotAlignments.Rd
man/plotChimeras.Rd
man/plotFreqHeatmap.Rd
man/plotVariants.Rd
man/rcAlns.Rd
man/readTargetBam.Rd
man/readsByPCRPrimer.Rd
man/readsToTarget.Rd
man/refFromAlns.Rd
man/reverseCigar.Rd
man/rmMultiPCRChimera.Rd
man/selectAlnRegionsHelpers.Rd
man/selectOps.Rd
man/seqsToAln.Rd
man/setDNATileColours.Rd
man/setMismatchTileColours.Rd
man/transformAlnsToLong.Rd
man/variantCounts.Rd
man/writeFastq.Rd
readme.Rmd
readme.html
readme.md
tests/testthat.R
tests/testthat/test-accessors.R
tests/testthat/test-annotate-plot.R
tests/testthat/test-initialisers.R
tests/testthat/test-narrowAlignments.R
tests/testthat/test-plotAlignments.R
tests/testthat/test-refsToAln.R
tests/testthat/test-seqsToAln.R
tests/testthat/test-utils.R
vignettes/user_guide.R
vignettes/user_guide.Rmd
