StructuralVariantAnnotation

DOI: 10.18129/B9.bioc.StructuralVariantAnnotation    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see StructuralVariantAnnotation.

Variant annotations for structural variants

Bioconductor version: 3.15

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>

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	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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_1.12.0.tar.gz
Windows Binary	StructuralVariantAnnotation_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	StructuralVariantAnnotation_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/StructuralVariantAnnotation
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/StructuralVariantAnnotation
Package Short Url	https://bioconductor.org/packages/StructuralVariantAnnotation/
Package Downloads Report	Download Stats