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VariantFiltering

This is the development version of VariantFiltering; for the stable release version, see VariantFiltering.

Filtering of coding and non-coding genetic variants


Bioconductor version: Development (3.19)

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.

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

Maintainer: Robert Castelo <robert.castelo at upf.edu>

Citation (from within R, enter citation("VariantFiltering")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("VariantFiltering")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VariantFiltering")
VariantFiltering: filter coding and non-coding genetic variants PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License Artistic-2.0
Depends R (>= 3.5.0), methods, BiocGenerics(>= 0.25.1), VariantAnnotation(>= 1.13.29)
Imports utils, stats, Biobase, S4Vectors(>= 0.9.25), IRanges(>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.3.6), GenomicRanges(>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools(>= 1.17.8), BSgenome, GenomicScores(>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree
System Requirements
URL https://github.com/rcastelo/VariantFiltering
Bug Reports https://github.com/rcastelo/VariantFiltering/issues
See More
Suggests RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
Linking To S4Vectors, IRanges, XVector, Biostrings
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package VariantFiltering_1.39.0.tar.gz
Windows Binary VariantFiltering_1.39.0.zip (64-bit only)
macOS Binary (x86_64) VariantFiltering_1.39.0.tgz
macOS Binary (arm64) VariantFiltering_1.39.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/VariantFiltering
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantFiltering
Bioc Package Browser https://code.bioconductor.org/browse/VariantFiltering/
Package Short Url https://bioconductor.org/packages/VariantFiltering/
Package Downloads Report Download Stats