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: Release (3.0)

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 1.2.7
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 3.0.0), methods, BiocGenerics(>= 0.11.3)
Imports DBI, RSQLite (>= 1.0.0), Biobase, S4Vectors, IRanges(>= 1.99.17), AnnotationDbi, BiocParallel, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.2.2), GenomicRanges(>= 1.17.19), GenomicFeatures, Rsamtools(>= 1.17.8), BSgenome, BSgenome.Hsapiens.UCSC.hg19, VariantAnnotation(>= 1.12.2), 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 https://github.com/rcastelo/VariantFiltering/issues
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_1.2.7.tar.gz
Windows Binary VariantFiltering_1.2.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VariantFiltering_1.2.7.tgz
Mac OS X 10.9 (Mavericks) VariantFiltering_1.2.7.tgz
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