TVTB: TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

AuthorKevin Rue-Albrecht [aut, cre]
Date of publicationNone
MaintainerKevin Rue-Albrecht <kevinrue67@gmail.com>
LicenseArtistic-2.0
Version1.0.2
https://github.com/kevinrue/TVTB

View on Bioconductor

Files in this package

TVTB/DESCRIPTION
TVTB/NAMESPACE
TVTB/R
TVTB/R/AllClasses.R TVTB/R/AllGenerics.R TVTB/R/Genotypes-class.R TVTB/R/TVTBparam-class.R TVTB/R/VcfFilterRules-class.R TVTB/R/addCountGenos-methods.R TVTB/R/addFrequencies-methods.R TVTB/R/addOverallFrequencies-methods.R TVTB/R/addPhenoLevelFrequencies-methods.R TVTB/R/countGenos-methods.R TVTB/R/dropInfo.R TVTB/R/readVcf-methods.R TVTB/R/show-methods.R TVTB/R/tSVE.R TVTB/R/variantsInSamples-methods.R TVTB/R/vepInPhenoLevel-methods.R
TVTB/README.md
TVTB/build
TVTB/build/partial.rdb
TVTB/build/vignette.rds
TVTB/inst
TVTB/inst/NEWS.Rd
TVTB/inst/badexamples
TVTB/inst/badexamples/chr3.dummy1.vcf.gz
TVTB/inst/badexamples/chr3.dummy2.vcf.gz
TVTB/inst/badexamples/noCSQ.vcf.gz
TVTB/inst/badexamples/noCSQ.vcf.gz.tbi
TVTB/inst/badexamples/pheno_NoOverlap.txt
TVTB/inst/badexamples/pheno_PartialOverlap.txt
TVTB/inst/doc
TVTB/inst/doc/Introduction.R
TVTB/inst/doc/Introduction.Rmd
TVTB/inst/doc/Introduction.html
TVTB/inst/doc/VcfFilterRules.R
TVTB/inst/doc/VcfFilterRules.Rmd
TVTB/inst/doc/VcfFilterRules.html
TVTB/inst/doc/tSVE.R
TVTB/inst/doc/tSVE.Rmd
TVTB/inst/doc/tSVE.html
TVTB/inst/extdata
TVTB/inst/extdata/SLC24A5.bed
TVTB/inst/extdata/chr15.phase3_integrated.vcf.gz
TVTB/inst/extdata/chr15.phase3_integrated.vcf.gz.tbi
TVTB/inst/extdata/integrated_samples.txt
TVTB/inst/extdata/moderate.vcf
TVTB/inst/extdata/moderate.vcf.gz
TVTB/inst/extdata/moderate.vcf.gz.tbi
TVTB/inst/extdata/moderate_pheno.txt
TVTB/inst/misc
TVTB/inst/misc/1kgenomes_SLC24A5_VEP.sh
TVTB/inst/misc/quickFilterTest.R
TVTB/inst/misc/subset_moderate_samples.R
TVTB/inst/misc/tSVE.xmind
TVTB/inst/sandbox
TVTB/inst/sandbox/densityVep-methods.R
TVTB/inst/sandbox/densityVep-methods.Rd
TVTB/inst/sandbox/tabulateVep-methods.R
TVTB/inst/sandbox/tabulateVep-methods.Rd
TVTB/inst/sandbox/test_densityVep-methods.R
TVTB/inst/sandbox/test_tabulateVep-methods.R
TVTB/inst/shinyApp
TVTB/inst/shinyApp/doc
TVTB/inst/shinyApp/doc/EnsDbFilter.Rd
TVTB/inst/shinyApp/doc/chr2file.Rd
TVTB/inst/shinyApp/doc/getEdb.Rd
TVTB/inst/shinyApp/ensembldbFunctions.R
TVTB/inst/shinyApp/fileParseFunctions.R
TVTB/inst/shinyApp/global.R
TVTB/inst/shinyApp/grangesParseFunctions.R
TVTB/inst/shinyApp/regions2vcf.R
TVTB/inst/shinyApp/server.R
TVTB/inst/shinyApp/serverRoutines.R
TVTB/inst/shinyApp/ui.R
TVTB/inst/shinyApp/www
TVTB/inst/shinyApp/www/bootstrap.css
TVTB/man
TVTB/man/Genotypes-class.Rd TVTB/man/TVTB-package.Rd TVTB/man/TVTBParam-class.Rd TVTB/man/VcfBasicRules-class.Rd TVTB/man/VcfFilterRules-class.Rd TVTB/man/addCountGenos-methods.Rd TVTB/man/addFrequencies-methods.Rd TVTB/man/addOverallFrequencies-methods.Rd TVTB/man/addPhenoLevelFrequencies-methods.Rd TVTB/man/countGenos-methods.Rd TVTB/man/dropInfo-methods.Rd TVTB/man/readVcf-methods.Rd TVTB/man/tSVE.Rd TVTB/man/variantsInSamples-methods.Rd TVTB/man/vepInPhenoLevel-methods.Rd
TVTB/tests
TVTB/tests/testthat
TVTB/tests/testthat.R
TVTB/tests/testthat/test_Genotypes-class.R
TVTB/tests/testthat/test_TVTBparam-class.R
TVTB/tests/testthat/test_VcfFilterRules-class.R
TVTB/tests/testthat/test_addCountGenos-methods.R
TVTB/tests/testthat/test_addFrequencies-methods.R
TVTB/tests/testthat/test_addOverallFrequencies-methods.R
TVTB/tests/testthat/test_addPhenoLevelFrequencies-methods.R
TVTB/tests/testthat/test_countGenos-methods.R
TVTB/tests/testthat/test_dropInfo.R
TVTB/tests/testthat/test_readVcf-methods.R
TVTB/tests/testthat/test_variantsInSamples-methods.R
TVTB/tests/testthat/test_vepInPhenoLevel-methods.R
TVTB/vignettes
TVTB/vignettes/Introduction.Rmd
TVTB/vignettes/TVTB.bib
TVTB/vignettes/VcfFilterRules.Rmd
TVTB/vignettes/tSVE.Rmd

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