To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("VariantFiltering")

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

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:

source("http://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)
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
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
System Requirements
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

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
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