Files in kevinrue/TVTB
TVTB: The VCF Tool Box
.BBSoptions
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/Genotypes-class.R
R/TVTBparam-class.R
R/VcfFilterRules-class.R
R/addCountGenos-methods.R
R/addFrequencies-methods.R
R/addOverallFrequencies-methods.R
R/addPhenoLevelFrequencies-methods.R
R/autodetectGenotypes.R
R/countGenos-methods.R
R/dropInfo.R
R/pairsInfo.R
R/parseCSQToGRanges.R
R/plotInfo.R
R/readVcf-methods.R
R/show-methods.R
R/tSVE.R
R/utils.R
R/variantsInSamples-methods.R
R/vepInPhenoLevel-methods.R
README.md
TVTB.Rproj
appveyor.yml
codecov.yml
inst/NEWS.Rd
inst/badexamples/chr3.dummy1.vcf.gz
inst/badexamples/chr3.dummy2.vcf.gz
inst/badexamples/noCSQ.vcf.gz
inst/badexamples/noCSQ.vcf.gz.tbi
inst/badexamples/pheno_NoOverlap.txt
inst/badexamples/pheno_OnlyColnames.txt
inst/badexamples/pheno_OnlyRownames.txt
inst/badexamples/pheno_PartialOverlap.txt
inst/extdata/ADH1B.bed
inst/extdata/SLC24A5.bed
inst/extdata/chr15.phase3_integrated.vcf.gz
inst/extdata/chr15.phase3_integrated.vcf.gz.tbi
inst/extdata/chr4.phase3_integrated.vcf.gz
inst/extdata/chr4.phase3_integrated.vcf.gz.tbi
inst/extdata/chr4.phase3_integrated.vcf_summary.html
inst/extdata/integrated_samples.txt
inst/extdata/moderate.vcf
inst/extdata/moderate.vcf.gz
inst/extdata/moderate.vcf.gz.tbi
inst/extdata/moderate_pheno.txt
inst/misc/1kgenomes_ADH1B_VEP.sh
inst/misc/1kgenomes_SLC24A5_VEP.sh
inst/misc/motivations_rules.rds
inst/sandbox/SKAT.R
inst/sandbox/densityVep-methods.R
inst/sandbox/densityVep-methods.Rd
inst/sandbox/tabulateVep-methods.R
inst/sandbox/tabulateVep-methods.Rd
inst/sandbox/test_densityVep-methods.R
inst/sandbox/test_tabulateVep-methods.R
inst/shinyApp/doc/EnsDbFilter.Rd
inst/shinyApp/doc/chr2file.Rd
inst/shinyApp/doc/getEdb.Rd
inst/shinyApp/ensembldbFunctions.R
inst/shinyApp/fileParseFunctions.R
inst/shinyApp/global.R
inst/shinyApp/grangesParseFunctions.R
inst/shinyApp/rds/parallel.rds
inst/shinyApp/regions2vcf.R
inst/shinyApp/server.R
inst/shinyApp/serverRoutines.R
inst/shinyApp/ui.R
inst/shinyApp/www/bootstrap.css
man/Genotypes-class.Rd
man/TVTB-package.Rd
man/TVTBParam-class.Rd
man/VcfBasicRules-class.Rd
man/VcfFilterRules-class.Rd
man/addCountGenos-methods.Rd
man/addFrequencies-methods.Rd
man/addOverallFrequencies-methods.Rd
man/addPhenoLevelFrequencies-methods.Rd
man/autodetectGenotypes.Rd
man/countGenos-methods.Rd
man/dropInfo-methods.Rd
man/figures/logo.png
man/pairsInfo-methods.Rd
man/parseCSQToGRanges.Rd
man/plotInfo-methods.Rd
man/readVcf-methods.Rd
man/tSVE.Rd
man/variantsInSamples-methods.Rd
man/vepInPhenoLevel-methods.Rd
tests/testthat.R
tests/testthat/test_Genotypes-class.R
tests/testthat/test_TVTBparam-class.R
tests/testthat/test_VcfFilterRules-class.R
tests/testthat/test_addCountGenos-methods.R
tests/testthat/test_addFrequencies-methods.R
tests/testthat/test_addOverallFrequencies-methods.R
tests/testthat/test_addPhenoLevelFrequencies-methods.R
tests/testthat/test_autodetectGenotypes-methods.R
tests/testthat/test_countGenos-methods.R
tests/testthat/test_dropInfo.R
tests/testthat/test_pairsInfo-methods.R
tests/testthat/test_plotInfo-methods.R
tests/testthat/test_readVcf-methods.R
tests/testthat/test_variantsInSamples-methods.R
tests/testthat/test_vepInPhenoLevel-methods.R
vignettes/Introduction.Rmd
vignettes/TVTB.bib
vignettes/VcfFilterRules.Rmd
vignettes/tSVE.Rmd
