VariantFiltering

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Filtering of coding and non-coding genetic variants

Bioconductor version: Development (3.24)

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], Joan Fernandez [ctb]

Maintainer: Robert Castelo <robert.castelo at upf.edu>

Citation (from within R, enter citation("VariantFiltering")):

Robert Castelo. VariantFiltering: Filtering of coding and non-coding genetic variants. doi:10.18129/B9.bioc.VariantFiltering, R package version 1.49.0, https://bioconductor.org/packages/VariantFiltering.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("VariantFiltering")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VariantFiltering")

VariantFiltering: filter coding and non-coding genetic variants	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version	1.49.0
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29)
Imports	utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome (>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1), shiny, shinythemes, shinyjs, DT, shinyTree
System Requirements
URL	https://github.com/rcastelo/VariantFiltering
Bug Reports	https://github.com/rcastelo/VariantFiltering/issues

Suggests	RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
Linking To	S4Vectors, IRanges, XVector, Biostrings
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	VariantFiltering_1.49.0.tar.gz
Windows Binary (x86_64)	VariantFiltering_1.49.0.zip
macOS Binary (big-sur-x86_64)	VariantFiltering_1.49.0.tgz
macOS Binary (sonoma-arm64)	VariantFiltering_1.49.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantFiltering
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VariantFiltering
Package Short Url	https://bioconductor.org/packages/VariantFiltering/
Package Downloads Report	Download Stats