Package: VariantFiltering 1.43.0

Robert Castelo

VariantFiltering: Filtering of coding and non-coding genetic variants

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

Authors:Robert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb], Joan Fernandez [ctb]

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NEWS

# Install 'VariantFiltering' in R:
install.packages('VariantFiltering', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rcastelo/variantfiltering/issues

On BioConductor:VariantFiltering-1.43.0(bioc 3.21)VariantFiltering-1.42.0(bioc 3.20)

geneticshomo_sapiensannotationsnpsequencinghighthroughputsequencing

6.13 score 4 stars 21 scripts 340 downloads 1 mentions 86 exports 169 dependencies

Last updated 23 days agofrom:779427d4c3. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-win-x86_64WARNINGNov 18 2024
R-4.5-linux-x86_64WARNINGNov 18 2024
R-4.4-win-x86_64WARNINGNov 18 2024
R-4.4-mac-x86_64WARNINGNov 18 2024
R-4.4-mac-aarch64WARNINGNov 18 2024
R-4.3-win-x86_64WARNINGNov 18 2024
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Exports:aaChangeTypeaaChangeType<-allVariantsannoGroupsautosomalDominantautosomalRecessiveHeterozygousautosomalRecessiveHomozygousbamFilesbamFiles<-browseVariantschange<-conservedPositionscutoffscutoffs<-dbSNPpresentdbSNPpresent<-deNovodownstreamdownstream<-filteredVariantsfiltersfilters<-filtersMetadataFiveSpliceSiteVariantsgenePhylostrataGenePhylostrataDbgenePhylostratumhumanGenesPhylostratainheritanceModelMAFpopMAFpop<-maxMAFmaxMAF<-minCUFCminCUFC<-minIntronLengthminIntronLength<-minPhastConsminPhastCons<-minPhylostratumminPhylostratum<-minScore3ssminScore3ss<-minScore5ssminScore5ss<-naMAFnaMAF<-OMIMpresentOMIMpresent<-paramreadAAradicalChangeMatrixreadWmreportVariantsresetSamplessamplessamples<-sequence_variant.gSOXPshowsoftFilterMatrixsoftFilterMatrix<-sogsortingssortings<-spliceSiteMatricesHumansummaryThreeSpliceSiteVariantsunrelatedIndividualsupstreamupstream<-variantConsequencevariantConsequence<-VariantFilteringParamvariantLocationvariantLocation<-variantLocationsvariantTypevariantType<-widthwmFilenamewmLocationswmLocations<-wmNamewmScorewmStrictLocationswmStrictLocations<-xLinked

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrDTensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGenomicScoresggplot2gluegraphgridExtragtableGvizHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesshinyshinyjsshinythemesshinyTreesnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioc

VariantFiltering: filter coding and non-coding genetic variants

Rendered fromusingVariantFiltering.Rnwusingutils::Sweaveon Nov 18 2024.

Last update: 2020-09-07
Started: 2014-03-31

Readme and manuals

Help Manual

Help pageTopics
Filtering of coding and non-coding genetic variantsVariantFiltering-package VariantFiltering
Autosomal dominant inheritance analysisautosomalDominant autosomalDominant,VariantFilteringParam-method
Autosomal recessive inheritance analysis: HeterozygousautosomalRecessiveHeterozygous autosomalRecessiveHeterozygous,VariantFilteringParam-method
Autosomal recessive inheritance analysis: HomozygousautosomalRecessiveHomozygous autosomalRecessiveHomozygous,VariantFilteringParam-method
De Novo variants analysisdeNovo deNovo,VariantFilteringParam-method
PhastConsDb classgenePhylostrata genePhylostrata,GenePhylostrataDb-method GenePhylostrataDb GenePhylostrataDb-class genePhylostratum genePhylostratum,GenePhylostrataDb,character-method genePhylostratum,GenePhylostrataDb,missing-method genePhylostratum,GenePhylostrataDb-method humanGenesPhylostrata organism,GenePhylostrataDb-method show,GenePhylostrataDb-method
Read matrix of amino acid radical changesreadAAradicalChangeMatrix
Analysis designed to be applied over a group of unrelated individualsunrelatedIndividuals unrelatedIndividuals,VariantFilteringParam-method
VariantFiltering parameter class$,VariantFilteringParam-method class:VariantFilteringParam cutoffs,VariantFilteringParam-method filters,VariantFilteringParam-method names,VariantFilteringParam-method sequence_variant.gSOXP show,VariantFilteringParam-method sog,VariantFilteringParam-method spliceSiteMatricesHuman VariantFilteringParam VariantFilteringParam-class variantLocations
VariantFilteringResults classallVariants allVariants,VariantFilteringResults-method annoGroups annoGroups,VariantFilteringResults-method bamFiles bamFiles,VariantFilteringResults-method bamFiles<- bamFiles<-,VariantFilteringResults,BamViews-method bamFiles<-,VariantFilteringResults-method browseVariants change change<- change<-,CutoffsList change<-,CutoffsList,ANY,character-method change<-,CutoffsList,ANY,integer-method change<-,CutoffsList,ANY,logical-method change<-,CutoffsList,ANY,numeric-method class:CutoffsList class:VariantFilteringResults cutoffs cutoffs,VariantFilteringResults-method cutoffs<- cutoffs<-,VariantFilteringResults,CutoffsList-method cutoffs<-,VariantFilteringResults,logical-method cutoffs<-,VariantFilteringResults-method CutoffsList CutoffsList-class filteredVariants filteredVariants,VariantFilteringResults-method filters filters,VariantFilteringResults-method filters<- filters<-,VariantFilteringResults-method filtersMetadata filtersMetadata,VariantFilteringParam-method filtersMetadata,VariantFilteringResults-method inheritanceModel inheritanceModel,VariantFilteringResults-method length length,VariantFilteringResults-method param param,VariantFilteringResults-method plot,VariantFilteringResults,ANY-method referenceGenome,VariantFilteringResults-method reportVariants reportVariants,VariantFilteringResults-method resetSamples resetSamples,VariantFilteringResults-method samples samples,VariantFilteringResults-method samples<- samples<-,VariantFilteringResults,character-method samples<-,VariantFilteringResults-method show,CompressedVRangesList-method show,VariantFilteringResults-method show,VariantFilteringResultsUI-method softFilterMatrix,VariantFilteringResults-method softFilterMatrix<-,VariantFilteringResults-method sog sog,VariantFilteringResults-method sortings sortings,VariantFilteringResults-method sortings<- sortings<-,VariantFilteringResults,CutoffsList-method summary,VariantFilteringResults-method VariantFilteringResults VariantFilteringResults-class
FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantTypedownstream downstream,FiveSpliceSiteVariants-method downstream,ThreeSpliceSiteVariants-method downstream<- downstream<-,FiveSpliceSiteVariants-method downstream<-,ThreeSpliceSiteVariants-method FiveSpliceSiteVariants FiveSpliceSiteVariants-class minIntronLength minIntronLength,FiveSpliceSiteVariants-method minIntronLength,ThreeSpliceSiteVariants-method minIntronLength<- minIntronLength<-,FiveSpliceSiteVariants-method minIntronLength<-,ThreeSpliceSiteVariants-method show,FiveSpliceSiteVariants-method show,ThreeSpliceSiteVariants-method ThreeSpliceSiteVariants ThreeSpliceSiteVariants-class upstream upstream,FiveSpliceSiteVariants-method upstream,ThreeSpliceSiteVariants-method upstream<- upstream<-,FiveSpliceSiteVariants-method upstream<-,ThreeSpliceSiteVariants-method
Weight matrix classconservedPositions conservedPositions,WeightMatrix-method readWm show,WeightMatrix-method WeightMatrix WeightMatrix-class width,WeightMatrix-method wmFilename wmFilename,WeightMatrix-method wmLocations wmLocations,WeightMatrix-method wmLocations<- wmLocations<-,WeightMatrix,character-method wmLocations<-,WeightMatrix-method wmName wmName,WeightMatrix-method wmScore wmScore,character,character-method wmScore,character,DNAStringSet-method wmScore,WeightMatrix,character-method wmScore,WeightMatrix,DNAStringSet-method wmStrictLocations wmStrictLocations,WeightMatrix-method wmStrictLocations<- wmStrictLocations<-,WeightMatrix,logical-method wmStrictLocations<-,WeightMatrix-method
X-Linked inheritance analysisxLinked xLinked,VariantFilteringParam-method