StructuralVariantAnnotation

DOI: 10.18129/B9.bioc.StructuralVariantAnnotation  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see StructuralVariantAnnotation.

Variant annotations for structural variants

Bioconductor version: 3.16

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Author: Daniel Cameron [aut, cre] , Ruining Dong [aut]

Maintainer: Daniel Cameron <daniel.l.cameron at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("StructuralVariantAnnotation")

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("StructuralVariantAnnotation")

 

HTML R Script Structural Variant Annotation Package
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.14.1
In Bioconductor since BioC 3.9 (R-3.6) (4 years)
License GPL-3 + file LICENSE
Depends GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0)
Imports assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb
LinkingTo
Suggests ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me svaNUMT, svaRetro
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package StructuralVariantAnnotation_1.14.1.tar.gz
Windows Binary StructuralVariantAnnotation_1.14.1.zip
macOS Binary (x86_64) StructuralVariantAnnotation_1.14.1.tgz
macOS Binary (arm64) StructuralVariantAnnotation_1.14.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/StructuralVariantAnnotation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/StructuralVariantAnnotation
Bioc Package Browser https://code.bioconductor.org/browse/StructuralVariantAnnotation/
Package Short Url https://bioconductor.org/packages/StructuralVariantAnnotation/
Package Downloads Report Download Stats

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