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StructuralVariantAnnotation

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

Variant annotations for structural variants


Bioconductor version: Development (3.19)

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 "4.4") 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

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
URL
See More
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_1.19.0.tar.gz
Windows Binary StructuralVariantAnnotation_1.19.0.zip
macOS Binary (x86_64) StructuralVariantAnnotation_1.19.0.tgz
macOS Binary (arm64) StructuralVariantAnnotation_1.19.0.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