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 is the development version of VariantFiltering; for the stable release version, see VariantFiltering.

Filtering of coding and non-coding genetic variants

Bioconductor version: Development (3.4)

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

Details

biocViews Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.9.13
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
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source VariantFiltering_1.9.13.tar.gz
Windows Binary VariantFiltering_1.9.13.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) VariantFiltering_1.9.13.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/VariantFiltering
Package Short Url http://bioconductor.org/packages/VariantFiltering/
Package Downloads Report Download Stats

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