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

 

   

Filtering of coding and non-coding genetic variants

Bioconductor version: Release (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_1.8.4.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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