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

Filtering of coding and non-coding genetic variants

Bioconductor version: 2.14

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: Dei M. Elurbe, Robert Castelo

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	1.0.4
In Bioconductor since	BioC 2.14 (R-3.1) (2 years)
License	Artistic-2.0
Depends	R (>= 3.0.0), methods, BiocGenerics(>= 0.9.1)
Imports	DBI, RSQLite (>= 0.8-1), Biobase, IRanges(>= 1.21.13), AnnotationDbi, BiocParallel, Biostrings(>= 2.29.19), GenomicRanges, Rsamtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, VariantAnnotation, shiny
LinkingTo	IRanges, XVector, Biostrings
Suggests	BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20120608, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
SystemRequirements
Enhances
URL
Depends On Me	MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg19
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	VariantFiltering_1.0.4.tar.gz
Windows Binary	VariantFiltering_1.0.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	VariantFiltering_1.0.4.tgz
Mac OS X 10.9 (Mavericks)	VariantFiltering_1.0.4.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/VariantFiltering/tree/release-2.14
Package Short Url	http://bioconductor.org/packages/VariantFiltering/
Package Downloads Report	Download Stats

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