VariantFiltering

DOI: 10.18129/B9.bioc.VariantFiltering    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see VariantFiltering.

Filtering of coding and non-coding genetic variants

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

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

 

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

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 2.14 (R-3.1) (5 years)
License	Artistic-2.0
Depends	R (>= 3.0.0), 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
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
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
SystemRequirements
Enhances
URL	https://github.com/rcastelo/VariantFiltering
BugReports	https://github.com/rcastelo/VariantFiltering/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	VariantFiltering_1.18.0.tar.gz
Windows Binary	VariantFiltering_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	VariantFiltering_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantFiltering
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VariantFiltering
Package Short Url	http://bioconductor.org/packages/VariantFiltering/
Package Downloads Report	Download Stats