To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

VariantFiltering

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see VariantFiltering.

Filtering of coding and non-coding genetic variants

Bioconductor version: 3.3

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>

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

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	1.8.6
In Bioconductor since	BioC 2.14 (R-3.1) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.0.0), methods, BiocGenerics(>= 0.13.8), VariantAnnotation(>= 1.13.29)
Imports	utils, DBI, RSQLite (>= 1.0.0), 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
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.phase3.hs37d5, MafDb.ExAC.r0.3.1.snvs.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	MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5b.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.1.nonTCGA.snvs.hs37d5, MafDb.ExAC.r0.3.1.snvs.hs37d5, MafDb.ExAC.r0.3.sites, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	VariantFiltering_1.8.6.tar.gz
Windows Binary	VariantFiltering_1.8.6.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks)	VariantFiltering_1.8.6.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/VariantFiltering/tree/release-3.3
Package Short Url	http://bioconductor.org/packages/VariantFiltering/
Package Downloads Report	Download Stats

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