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 3.2 of Bioconductor; for the stable, up-to-date release version, see VariantFiltering.

Filtering of coding and non-coding genetic variants

Bioconductor version: 3.2

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minimum 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		VariantFiltering: filter coding and non-coding genetic variants
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.6.21
In Bioconductor since	BioC 2.14 (R-3.1) (2 years)
License	Artistic-2.0
Depends	R (>= 3.0.0), methods, BiocGenerics(>= 0.13.8), VariantAnnotation(>= 1.13.29)
Imports	DBI, RSQLite (>= 1.0.0), Biobase, S4Vectors(>= 0.7.21), IRanges(>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.3.6), GenomicRanges(>= 1.19.13), GenomicFeatures, Rsamtools(>= 1.17.8), BSgenome, Gviz, shiny
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
Suggests	BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20120608, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, 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.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ALL.wgs.phase3.release.v5b.20130502, MafDb.ESP6500SI.V2.SSA137, 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_1.6.21.tar.gz
Windows Binary	VariantFiltering_1.6.20.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	VariantFiltering_1.6.4.tgz
Mac OS X 10.9 (Mavericks)	VariantFiltering_1.6.21.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/VariantFiltering/tree/release-3.2
Package Short Url	http://bioconductor.org/packages/VariantFiltering/
Package Downloads Report	Download Stats

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