StructuralVariantAnnotation

This is the released version of StructuralVariantAnnotation; for the devel version, see StructuralVariantAnnotation.

Variant annotations for structural variants

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DOI: 10.18129/B9.bioc.StructuralVariantAnnotation

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0002-0951-7116 , Ruining Dong [aut] ORCID iD ORCID: 0000-0003-1433-0484

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")
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 1.26.0

In Bioconductor since BioC 3.9 (R-3.6) (6.5 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

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Enhances

Depends On Me svaNUMT, svaRetro

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Package Archives

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

Source Package StructuralVariantAnnotation_1.26.0.tar.gz

Windows Binary (x86_64) StructuralVariantAnnotation_1.25.0.zip (64-bit only)

macOS Binary (x86_64) StructuralVariantAnnotation_1.26.0.tgz

macOS Binary (arm64) StructuralVariantAnnotation_1.26.0.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/

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