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.

AuthorRobert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb]
Date of publicationNone
MaintainerRobert Castelo <robert.castelo@upf.edu>
LicenseArtistic-2.0
Version1.10.1
https://github.com/rcastelo/VariantFiltering

View on Bioconductor

Files in this package

VariantFiltering/DESCRIPTION
VariantFiltering/NAMESPACE
VariantFiltering/NEWS
VariantFiltering/R
VariantFiltering/R/AllClasses.R VariantFiltering/R/AllGeneric.R VariantFiltering/R/AllUtilities.R VariantFiltering/R/annotationEngine.R VariantFiltering/R/autosomalDominant.R VariantFiltering/R/autosomalRecessiveHeterozygous.R VariantFiltering/R/autosomalRecessiveHomozygous.R VariantFiltering/R/deNovo.R VariantFiltering/R/defaultFilters.R VariantFiltering/R/methods-GenePhyloStrataDb.R VariantFiltering/R/methods-MafDb.R VariantFiltering/R/methods-MafDb2.R VariantFiltering/R/methods-PhastConsDb.R VariantFiltering/R/methods-SequenceOntology.R VariantFiltering/R/methods-VariantFilteringParam.R VariantFiltering/R/methods-VariantFilteringResults.R VariantFiltering/R/methods-VariantType-class.R VariantFiltering/R/methods-Visualization.R VariantFiltering/R/methods-WeightMatrix.R VariantFiltering/R/methods-locateVariants.R VariantFiltering/R/scoreBindingSiteVariants.R VariantFiltering/R/tabPanelAbout.R VariantFiltering/R/unrelatedIndividuals.R VariantFiltering/R/xLinked.R VariantFiltering/R/zzz.R
VariantFiltering/build
VariantFiltering/build/vignette.rds
VariantFiltering/inst
VariantFiltering/inst/CITATION
VariantFiltering/inst/doc
VariantFiltering/inst/doc/usingVariantFiltering.R
VariantFiltering/inst/doc/usingVariantFiltering.Rnw
VariantFiltering/inst/doc/usingVariantFiltering.pdf
VariantFiltering/inst/extdata
VariantFiltering/inst/extdata/AA_chemical_properties_HanadaGojoboriLi2006.tsv
VariantFiltering/inst/extdata/CEUtrio.ped
VariantFiltering/inst/extdata/CEUtrio.vcf.bgz
VariantFiltering/inst/extdata/CEUtrio.vcf.bgz.tbi
VariantFiltering/inst/extdata/NA12878.subset.bam
VariantFiltering/inst/extdata/NA12878.subset.bam.bai
VariantFiltering/inst/extdata/NA12891.subset.bam
VariantFiltering/inst/extdata/NA12891.subset.bam.bai
VariantFiltering/inst/extdata/NA12892.subset.bam
VariantFiltering/inst/extdata/NA12892.subset.bam.bai
VariantFiltering/inst/extdata/README_SequenceOntology
VariantFiltering/inst/extdata/README_humanGenesPhylostrata
VariantFiltering/inst/extdata/hsap.acceptors.hcmc10_15_1.ibn
VariantFiltering/inst/extdata/hsap.donors.hcmc10_15_1.ibn
VariantFiltering/inst/extdata/humanCodonUsage.txt
VariantFiltering/inst/extdata/humanEnsGenePhylostrata.rda
VariantFiltering/inst/extdata/sequence_variant.gSOXPapril2016.rds
VariantFiltering/inst/extdata/uind.rds
VariantFiltering/inst/unitTests
VariantFiltering/inst/unitTests/test_VariantFilteringParam-methods.R
VariantFiltering/inst/unitTests/test_inheritance-models.R
VariantFiltering/inst/unitTests/test_location-methods.R
VariantFiltering/man
VariantFiltering/man/GenePhylostrataDb-class.Rd VariantFiltering/man/MafDb-class.Rd VariantFiltering/man/MafDb2-class.Rd VariantFiltering/man/PhastConsDb-class.Rd VariantFiltering/man/VariantFiltering-defunct.Rd VariantFiltering/man/VariantFiltering-deprecated.Rd VariantFiltering/man/VariantFiltering-package.Rd VariantFiltering/man/VariantFilteringParam-class.Rd VariantFiltering/man/VariantFilteringResults-class.Rd VariantFiltering/man/VariantType-class.Rd VariantFiltering/man/WeightMatrix-class.Rd VariantFiltering/man/autosomalDominant.Rd VariantFiltering/man/autosomalRecessiveHeterozygous.Rd VariantFiltering/man/autosomalRecessiveHomozygous.Rd VariantFiltering/man/deNovo.Rd VariantFiltering/man/readAAradicalChangeMatrix.Rd VariantFiltering/man/unrelatedIndividuals.Rd VariantFiltering/man/xLinked.Rd
VariantFiltering/src
VariantFiltering/src/Biostrings_stubs.c
VariantFiltering/src/R_init_VariantFiltering.c
VariantFiltering/src/VariantFiltering.h
VariantFiltering/src/methods-WeightMatrix.c
VariantFiltering/tests
VariantFiltering/tests/runTests.R
VariantFiltering/vignettes
VariantFiltering/vignettes/shinysnapshotVariantFiltering.jpg
VariantFiltering/vignettes/usingVariantFiltering.Rnw

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