StructuralVariantAnnotation

This is the development version of StructuralVariantAnnotation; for the stable release version, see StructuralVariantAnnotation.

Variant annotations for structural variants

Bioconductor version: Development (3.21)

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] (ORCID: ), Ruining Dong [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version	1.23.0
In Bioconductor since	BioC 3.9 (R-3.6) (5.5 years)
License	GPL-3 + file LICENSE
Depends	GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0)
Imports	assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb
System Requirements
URL

Suggests	ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19
Linking To
Enhances
Depends On Me	svaNUMT, svaRetro
Imports Me
Suggests Me	shiny.gosling
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	StructuralVariantAnnotation_1.23.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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