├── .gitignore ├── CrispRvariants.Rproj ├── DESCRIPTION ├── NAMESPACE ├── NEWS.Rmd ├── R ├── CrisprRun.R ├── CrisprSet.R ├── abifToFastq.R ├── accessors.R ├── barplotAlleleFreqs.R ├── crispRvariants_data.R ├── excludeFromBam.R ├── findChimeras.R ├── initialisers.R ├── plotAlignments.R ├── plotChimeras.R ├── plotFreqHeatmap.R ├── plotVariants.R ├── readsByPCRPrimer.R ├── reverseCigar.R ├── seqsToAln.R ├── utils.R └── writeFastq.R ├── data └── gol_clutch1.rda ├── inst ├── NEWS.Rmd └── extdata │ ├── Danio_rerio.Zv9.73.gol.sqlite │ ├── GRCz10_81_ptena_txdb.sqlite │ ├── IM2033.ab1 │ ├── ab1 │ └── ptena │ │ └── phenotype │ │ └── embryo1 │ │ └── AB2001.ab1 │ ├── bam │ ├── ab1_ptena_phenotype_embryo_1_s.bam │ ├── ab1_ptena_phenotype_embryo_1_s.bam.bai │ ├── ab1_ptena_phenotype_embryo_2_s.bam │ ├── ab1_ptena_phenotype_embryo_2_s.bam.bai │ ├── ab1_ptena_uninjected_embryo_1_s.bam │ ├── ab1_ptena_uninjected_embryo_1_s.bam.bai │ ├── ab1_ptena_wildtype_looking_embryo_1_s.bam │ ├── ab1_ptena_wildtype_looking_embryo_1_s.bam.bai │ ├── ab1_ptena_wildtype_looking_embryo_2_s.bam │ └── ab1_ptena_wildtype_looking_embryo_2_s.bam.bai │ ├── bed │ └── guide.bed │ ├── cntnap2b_test_data.fastq.gz │ ├── cntnap2b_test_data_guide.bed │ ├── cntnap2b_test_data_s.bam │ ├── gol_F1_clutch_1_embryo_1_s.bam │ ├── gol_F1_clutch_1_embryo_1_s.bam.bai │ ├── gol_F1_clutch_1_embryo_2_s.bam │ ├── gol_F1_clutch_1_embryo_2_s.bam.bai │ ├── gol_F1_clutch_1_embryo_3_s.bam │ ├── gol_F1_clutch_1_embryo_3_s.bam.bai │ ├── gol_F1_clutch_1_embryo_4_s.bam │ ├── gol_F1_clutch_1_embryo_4_s.bam.bai │ ├── gol_F1_clutch_1_embryo_5_s.bam │ ├── gol_F1_clutch_1_embryo_5_s.bam.bai │ ├── gol_F1_clutch_1_embryo_6_s.bam │ ├── gol_F1_clutch_1_embryo_6_s.bam.bai │ ├── gol_F1_clutch_1_embryo_7_s.bam │ ├── gol_F1_clutch_1_embryo_7_s.bam.bai │ ├── gol_F1_clutch_1_embryo_8_s.bam │ ├── gol_F1_clutch_1_embryo_8_s.bam.bai │ ├── gol_F1_clutch_2_embryo_4_s.bam │ ├── gol_F1_clutch_2_embryo_4_s.bam.bai │ ├── gol_F1_metadata.txt │ ├── gol_F1_metadata_small.txt │ ├── metadata │ └── metadata.xls │ ├── ptena_GRCHz10_ref.rda │ └── wtx_Sanger.png ├── man ├── CrisprRun-class.Rd ├── CrisprSet-class.Rd ├── abifToFastq.Rd ├── addClipped.Rd ├── annotateGenePlot.Rd ├── arrangePlots.Rd ├── barplotAlleleFreqs.Rd ├── collapsePairs.Rd ├── dispatchDots.Rd ├── excludeFromBam.Rd ├── findChimeras.Rd ├── findSNVs.Rd ├── getChimeras.Rd ├── gol_clutch1.Rd ├── indelCounts.Rd ├── mergeCrisprSets.Rd ├── mutationEfficiency.Rd ├── narrowAlignments.Rd ├── plotAlignments.Rd ├── plotChimeras.Rd ├── plotFreqHeatmap.Rd ├── plotVariants.Rd ├── rcAlns.Rd ├── readTargetBam.Rd ├── readsByPCRPrimer.Rd ├── readsToTarget.Rd ├── reverseCigar.Rd ├── rmMultiPCRChimera.Rd ├── seqsToAln.Rd ├── setDNATileColours.Rd ├── transformAlnsToLong.Rd ├── variantCounts.Rd └── writeFastq.Rd ├── readme.Rmd ├── readme.html ├── readme.md ├── tests ├── testthat.R └── testthat │ ├── test-initialisers.R │ ├── test-narrowAlignments.R │ └── test-utils.R └── vignettes ├── user_guide.Rmd └── user_guide.pdf /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/.gitignore -------------------------------------------------------------------------------- /CrispRvariants.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/CrispRvariants.Rproj -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.Rmd: -------------------------------------------------------------------------------- 1 | # CrispRVariants 0.99.1 -------------------------------------------------------------------------------- /R/CrisprRun.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/CrisprRun.R -------------------------------------------------------------------------------- /R/CrisprSet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/CrisprSet.R -------------------------------------------------------------------------------- /R/abifToFastq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/abifToFastq.R -------------------------------------------------------------------------------- /R/accessors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/accessors.R -------------------------------------------------------------------------------- /R/barplotAlleleFreqs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/barplotAlleleFreqs.R -------------------------------------------------------------------------------- /R/crispRvariants_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/crispRvariants_data.R -------------------------------------------------------------------------------- /R/excludeFromBam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/excludeFromBam.R -------------------------------------------------------------------------------- /R/findChimeras.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/findChimeras.R -------------------------------------------------------------------------------- /R/initialisers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/initialisers.R -------------------------------------------------------------------------------- /R/plotAlignments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/plotAlignments.R -------------------------------------------------------------------------------- /R/plotChimeras.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/plotChimeras.R -------------------------------------------------------------------------------- /R/plotFreqHeatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/plotFreqHeatmap.R -------------------------------------------------------------------------------- /R/plotVariants.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/plotVariants.R -------------------------------------------------------------------------------- /R/readsByPCRPrimer.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/readsByPCRPrimer.R -------------------------------------------------------------------------------- /R/reverseCigar.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/reverseCigar.R -------------------------------------------------------------------------------- /R/seqsToAln.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/seqsToAln.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/utils.R -------------------------------------------------------------------------------- /R/writeFastq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/R/writeFastq.R -------------------------------------------------------------------------------- /data/gol_clutch1.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/data/gol_clutch1.rda -------------------------------------------------------------------------------- /inst/NEWS.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/NEWS.Rmd -------------------------------------------------------------------------------- /inst/extdata/Danio_rerio.Zv9.73.gol.sqlite: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/Danio_rerio.Zv9.73.gol.sqlite -------------------------------------------------------------------------------- /inst/extdata/GRCz10_81_ptena_txdb.sqlite: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/GRCz10_81_ptena_txdb.sqlite -------------------------------------------------------------------------------- /inst/extdata/IM2033.ab1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/IM2033.ab1 -------------------------------------------------------------------------------- /inst/extdata/ab1/ptena/phenotype/embryo1/AB2001.ab1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/ab1/ptena/phenotype/embryo1/AB2001.ab1 -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam -------------------------------------------------------------------------------- /inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/bed/guide.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/bed/guide.bed -------------------------------------------------------------------------------- /inst/extdata/cntnap2b_test_data.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/cntnap2b_test_data.fastq.gz -------------------------------------------------------------------------------- /inst/extdata/cntnap2b_test_data_guide.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/cntnap2b_test_data_guide.bed -------------------------------------------------------------------------------- /inst/extdata/cntnap2b_test_data_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/cntnap2b_test_data_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_1_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_1_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_1_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_1_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_2_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_2_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_2_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_2_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_3_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_3_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_3_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_3_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_4_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_4_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_4_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_4_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_5_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_5_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_5_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_5_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_6_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_6_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_6_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_6_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_7_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_7_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_7_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_7_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_8_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_8_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_1_embryo_8_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_1_embryo_8_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_2_embryo_4_s.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_2_embryo_4_s.bam -------------------------------------------------------------------------------- /inst/extdata/gol_F1_clutch_2_embryo_4_s.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_clutch_2_embryo_4_s.bam.bai -------------------------------------------------------------------------------- /inst/extdata/gol_F1_metadata.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_metadata.txt -------------------------------------------------------------------------------- /inst/extdata/gol_F1_metadata_small.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/gol_F1_metadata_small.txt -------------------------------------------------------------------------------- /inst/extdata/metadata/metadata.xls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/metadata/metadata.xls -------------------------------------------------------------------------------- /inst/extdata/ptena_GRCHz10_ref.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/ptena_GRCHz10_ref.rda -------------------------------------------------------------------------------- /inst/extdata/wtx_Sanger.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/inst/extdata/wtx_Sanger.png -------------------------------------------------------------------------------- /man/CrisprRun-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/CrisprRun-class.Rd -------------------------------------------------------------------------------- /man/CrisprSet-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/CrisprSet-class.Rd -------------------------------------------------------------------------------- /man/abifToFastq.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/abifToFastq.Rd -------------------------------------------------------------------------------- /man/addClipped.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/addClipped.Rd -------------------------------------------------------------------------------- /man/annotateGenePlot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/annotateGenePlot.Rd -------------------------------------------------------------------------------- /man/arrangePlots.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/arrangePlots.Rd -------------------------------------------------------------------------------- /man/barplotAlleleFreqs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/barplotAlleleFreqs.Rd -------------------------------------------------------------------------------- /man/collapsePairs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/collapsePairs.Rd -------------------------------------------------------------------------------- /man/dispatchDots.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/dispatchDots.Rd -------------------------------------------------------------------------------- /man/excludeFromBam.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/excludeFromBam.Rd -------------------------------------------------------------------------------- /man/findChimeras.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/findChimeras.Rd -------------------------------------------------------------------------------- /man/findSNVs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/findSNVs.Rd -------------------------------------------------------------------------------- /man/getChimeras.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/getChimeras.Rd -------------------------------------------------------------------------------- /man/gol_clutch1.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/gol_clutch1.Rd -------------------------------------------------------------------------------- /man/indelCounts.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/indelCounts.Rd -------------------------------------------------------------------------------- /man/mergeCrisprSets.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/mergeCrisprSets.Rd -------------------------------------------------------------------------------- /man/mutationEfficiency.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/mutationEfficiency.Rd -------------------------------------------------------------------------------- /man/narrowAlignments.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/narrowAlignments.Rd -------------------------------------------------------------------------------- /man/plotAlignments.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/plotAlignments.Rd -------------------------------------------------------------------------------- /man/plotChimeras.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/plotChimeras.Rd -------------------------------------------------------------------------------- /man/plotFreqHeatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/plotFreqHeatmap.Rd -------------------------------------------------------------------------------- /man/plotVariants.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/plotVariants.Rd -------------------------------------------------------------------------------- /man/rcAlns.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/rcAlns.Rd -------------------------------------------------------------------------------- /man/readTargetBam.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/readTargetBam.Rd -------------------------------------------------------------------------------- /man/readsByPCRPrimer.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/readsByPCRPrimer.Rd -------------------------------------------------------------------------------- /man/readsToTarget.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/readsToTarget.Rd -------------------------------------------------------------------------------- /man/reverseCigar.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/reverseCigar.Rd -------------------------------------------------------------------------------- /man/rmMultiPCRChimera.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/rmMultiPCRChimera.Rd -------------------------------------------------------------------------------- /man/seqsToAln.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/seqsToAln.Rd -------------------------------------------------------------------------------- /man/setDNATileColours.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/setDNATileColours.Rd -------------------------------------------------------------------------------- /man/transformAlnsToLong.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/transformAlnsToLong.Rd -------------------------------------------------------------------------------- /man/variantCounts.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/variantCounts.Rd -------------------------------------------------------------------------------- /man/writeFastq.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/man/writeFastq.Rd -------------------------------------------------------------------------------- /readme.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/readme.Rmd -------------------------------------------------------------------------------- /readme.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/readme.html -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/readme.md -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-initialisers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/tests/testthat/test-initialisers.R -------------------------------------------------------------------------------- /tests/testthat/test-narrowAlignments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/tests/testthat/test-narrowAlignments.R -------------------------------------------------------------------------------- /tests/testthat/test-utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/tests/testthat/test-utils.R -------------------------------------------------------------------------------- /vignettes/user_guide.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/vignettes/user_guide.Rmd -------------------------------------------------------------------------------- /vignettes/user_guide.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/markrobinsonuzh/CrispRVariants/HEAD/vignettes/user_guide.pdf --------------------------------------------------------------------------------