VariantFiltering

DOI: 10.18129/B9.bioc.VariantFiltering    

Filtering of coding and non-coding genetic variants

Bioconductor version: Release (3.6)

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]

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VariantFiltering")

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	1.14.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 years)
License	Artistic-2.0
Depends	R (>= 3.0.0), methods, BiocGenerics(>= 0.13.8), VariantAnnotation(>= 1.13.29)
Imports	utils, 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, Gviz, shiny, GenomicScores(>= 1.0.0)
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
Build Report

Package Archives

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

Source Package	VariantFiltering_1.14.0.tar.gz
Windows Binary	VariantFiltering_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	VariantFiltering_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantFiltering
Package Short Url	http://bioconductor.org/packages/VariantFiltering/
Package Downloads Report	Download Stats