Package: TVTB 1.33.0
Kevin Rue-Albrecht
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).
Authors:
TVTB_1.33.0.tar.gz
TVTB_1.33.0.zip(r-4.5)TVTB_1.33.0.zip(r-4.4)TVTB_1.33.0.zip(r-4.3)
TVTB_1.33.0.tgz(r-4.5-any)TVTB_1.33.0.tgz(r-4.4-any)TVTB_1.33.0.tgz(r-4.3-any)
TVTB_1.33.0.tar.gz(r-4.5-noble)TVTB_1.33.0.tar.gz(r-4.4-noble)
TVTB_1.33.0.tgz(r-4.4-emscripten)TVTB_1.33.0.tgz(r-4.3-emscripten)
TVTB.pdf |TVTB.html✨
TVTB/json (API)
NEWS
| # Install 'TVTB' in R: |
| install.packages('TVTB', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kevinrue/tvtb/issues
On BioConductor:TVTB-1.33.0(bioc 3.21)TVTB-1.32.0(bioc 3.20)
softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching
Last updated 4 months agofrom:9b5085b997. Checks:3 OK, 5 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 16 2025 |
| R-4.5-win | NOTE | Feb 16 2025 |
| R-4.5-mac | NOTE | Feb 16 2025 |
| R-4.5-linux | NOTE | Feb 16 2025 |
| R-4.4-win | NOTE | Feb 16 2025 |
| R-4.4-mac | NOTE | Feb 16 2025 |
| R-4.3-win | OK | Feb 16 2025 |
| R-4.3-mac | OK | Feb 16 2025 |
Exports:aafaaf<-activeactive<-addCountGenosaddFrequenciesaddOverallFrequenciesaddPhenoLevelFrequenciesaltalt<-appendautodetectGenotypesbpbp<-carriercolDatacolData<-countGenosdropInfoevalevalSeparatelyfixedgenogenosgenos<-Genotypesheaderheader<-hethet<-infoinfo<-mafmaf<-mcolsmetadatametadata<-pairsInfoparseCSQToGRangesplotInforangesranges<-readVcfrefref<-ScanVcfParamsubsetByFiltersuffixsvpsvp<-tSVETVTBparamtypevariantsInSamplesVcfFilterRulesVcfFixedRulesVcfInfoRulesVcfVepRulesvepvep<-vepInPhenoLevel
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggplot2ggstatsgluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryaml
Introduction to TVTB
Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Feb 16 2025.Last update: 2018-07-20
Started: 2016-10-13
The Shiny Variant Explorer
Rendered fromtSVE.Rmdusingknitr::rmarkdownon Feb 16 2025.Last update: 2020-04-11
Started: 2016-10-13
VCF filter rules
Rendered fromVcfFilterRules.Rmdusingknitr::rmarkdownon Feb 16 2025.Last update: 2024-07-04
Started: 2016-10-13
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| TVTB: The VCF Tool Box | TVTB-package |
| Add count of genotypes to INFO field | addCountGenos addCountGenos,ExpandedVCF-method addCountGenos-methods |
| Group-level genotypes counts and allele frequencies | addFrequencies addFrequencies,ExpandedVCF,character-method addFrequencies,ExpandedVCF,list-method addFrequencies,ExpandedVCF,missing-method addFrequencies-methods |
| Overall genotypes counts and allele frequencies | addOverallFrequencies addOverallFrequencies,ExpandedVCF-method addOverallFrequencies-methods |
| Genotypes and allele frequencies for a given phenotype level | addPhenoLevelFrequencies addPhenoLevelFrequencies,ExpandedVCF-method addPhenoLevelFrequencies-methods |
| Define genotypes in the TVTBparam metadata slot | autodetectGenotypes autodetectGenotypes,VCF-method autodetectGenotypes-methods |
| Count occurences of genotypes | countGenos countGenos,ExpandedVCF-method countGenos-methods |
| Remove INFO keys from VCF objects | dropInfo dropInfo,VCF-method dropInfo-methods |
| Genotypes class objects | alt,Genotypes-method alt<-,Genotypes,character-method carrier carrier,Genotypes-method class:Genotypes genos genos,Genotypes-method Genotypes Genotypes-class Genotypes-methods het het,Genotypes-method het<- het<-,Genotypes,character-method initialize,Genotypes-method ref,Genotypes-method ref<-,Genotypes,character-method suffix suffix,Genotypes-method |
| Plot an INFO metric on a genomic axis. | pairsInfo pairsInfo,VCF-method pairsInfo-methods |
| Parse the CSQ column of a VCF object into a GRanges object | parseCSQToGRanges parseCSQToGRanges,VCF-method |
| Plot an INFO metric on a genomic axis. | plotInfo plotInfo,VCF-method plotInfo-methods |
| Read VCF files | readVcf,character,TVTBparam-method readVcf,TabixFile,TVTBparam-method |
| The Shiny Variant Explorer (tSVE) web-application | tSVE |
| TVTBparam class objects | aaf aaf,TVTBparam-method aaf<- aaf<-,TVTBparam,character-method alt,TVTBparam-method alt<-,TVTBparam,character-method alt<-,TVTBparam,list-method bp bp,TVTBparam-method bp<- bp<-,TVTBparam,BiocParallelParam-method carrier,TVTBparam-method class:TVTBparam genos,TVTBparam-method genos<- genos<-,TVTBparam,Genotypes-method het,TVTBparam-method het<-,TVTBparam,character-method het<-,TVTBparam,list-method initialize,TVTBparam-method maf maf,TVTBparam-method maf<- maf<-,TVTBparam,character-method ranges ranges,TVTBparam-method ranges<- ranges<-,TVTBparam,GRangesList-method ref,TVTBparam-method ref<-,TVTBparam,character-method ref<-,TVTBparam,list-method suffix,TVTBparam-method svp svp,TVTBparam-method svp<- svp<-,TVTBparam,ScanVcfParam-method TVTBparam TVTBparam-class TVTBparam-methods vep vep,TVTBparam-method vep<- vep<-,TVTBparam,character-method |
| Identify variants observed in samples | variantsInSamples variantsInSamples,ExpandedVCF-method variantsInSamples-methods |
| VCF filters class objects sub-types | append,VcfFixedRules,FilterRules-method append,VcfInfoRules,FilterRules-method append,VcfVepRules,FilterRules-method c,VcfFixedRules-method c,VcfInfoRules-method c,VcfVepRules-method class:VcfFixedRules class:VcfInfoRules class:VcfVepRules eval,VcfFixedRules,VCF-method eval,VcfInfoRules,VCF-method eval,VcfVepRules,VCF-method initialize,VcfFixedRules-method initialize,VcfInfoRules-method initialize,VcfVepRules-method type,FilterRules-method type,VcfFixedRules-method type,VcfInfoRules-method type,VcfVepRules-method VcfFixedRules VcfFixedRules-class VcfInfoRules VcfInfoRules-class VcfVepRules VcfVepRules-class vep,FilterRules-method vep,VcfFixedRules-method vep,VcfInfoRules-method vep,VcfVepRules-method vep<-,VcfVepRules,character-method [,VcfFixedRules,ANY,ANY-method [,VcfInfoRules,ANY,ANY-method [,VcfVepRules,ANY,ANY-method [<-,VcfFixedRules,numeric,missing,VcfFixedRules-method [<-,VcfInfoRules,numeric,missing,VcfInfoRules-method [<-,VcfVepRules,numeric,missing,VcfVepRules-method [[,VcfFixedRules,ANY,ANY-method [[,VcfInfoRules,ANY,ANY-method [[,VcfVepRules,ANY,ANY-method [[<-,VcfFixedRules,ANY,ANY-method [[<-,VcfInfoRules,ANY,ANY-method [[<-,VcfVepRules,ANY,ANY-method |
| VcfFilterRules class objects | append,VcfFilterRules,FilterRules-method c,VcfFilterRules-method class:VcfFilterRules eval,VcfFilterRules,VCF-method initialize,VcfFilterRules-method type,VcfFilterRules-method VcfFilterRules VcfFilterRules-class vep,VcfFilterRules-method vep<-,VcfFilterRules,character-method [,VcfFilterRules,ANY,ANY,ANY-method [,VcfFilterRules,ANY,ANY,logical-method [,VcfFilterRules,ANY,ANY,missing-method [<-,VcfFilterRules,numeric,missing,VcfFilterRules-method [<-,VcfFilterRules,numeric,missing,VcfFixedRules-method [<-,VcfFilterRules,numeric,missing,VcfInfoRules-method [<-,VcfFilterRules,numeric,missing,VcfVepRules-method [[,VcfFilterRules,ANY,ANY-method [[<-,VcfFilterRules,ANY,ANY-method |
| VEP predictions of variants observed in samples | vepInPhenoLevel vepInPhenoLevel,ExpandedVCF-method vepInPhenoLevel-methods |
