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VariantFiltering
This is thereleased version of VariantFiltering; for the devel version, seeVariantFiltering.
Filtering of coding and non-coding genetic variants
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("VariantFiltering")For older versions of R, please refer to the appropriateBioconductor 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 | 1.46.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (11.5 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | VariantFiltering_1.46.0.tar.gz |
| Windows Binary (x86_64) | VariantFiltering_1.46.0.zip |
| macOS Binary (x86_64) | VariantFiltering_1.46.0.tgz |
| macOS Binary (arm64) | VariantFiltering_1.46.0.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 |