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 (3.20)
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 "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software |
Version | 1.41.0 |
In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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, 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_1.41.0.tar.gz |
Windows Binary | VariantFiltering_1.41.0.zip (64-bit only) |
macOS Binary (x86_64) | VariantFiltering_1.41.0.tgz |
macOS Binary (arm64) | VariantFiltering_1.41.0.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 |