VariantFiltering
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see VariantFiltering.
Filtering of coding and non-coding genetic variants
Bioconductor version: 3.9
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("VariantFiltering")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0), 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, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.3.6), GenomicRanges(>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools(>= 1.17.8), BSgenome, GenomicScores(>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree |
| System Requirements | |
| URL | https://github.com/rcastelo/VariantFiltering |
| Bug Reports | https://github.com/rcastelo/VariantFiltering/issues |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VariantFiltering_1.20.0.tar.gz |
| Windows Binary | VariantFiltering_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | VariantFiltering_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VariantFiltering |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VariantFiltering |
| Bioc Package Browser | https://code.bioconductor.org/browse/VariantFiltering/ |
| Package Short Url | https://bioconductor.org/packages/VariantFiltering/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |