StructuralVariantAnnotation

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see StructuralVariantAnnotation.

Variant annotations for structural variants

DOI: 10.18129/B9.bioc.StructuralVariantAnnotation

Bioconductor version: 3.9

StructuralVariantAnnotation 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 "3.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation

Version 1.0.0

In Bioconductor since BioC 3.9 (R-3.6) (5 years)

License GPL-3

Depends GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 3.6.0)

Imports assertthat, Biostrings, stringr, dplyr, methods, rlang

System Requirements

URL

Suggests BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment

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Package Archives

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

Source Package StructuralVariantAnnotation_1.0.0.tar.gz

Windows Binary StructuralVariantAnnotation_1.0.0.zip

Mac OS X 10.11 (El Capitan) StructuralVariantAnnotation_1.0.0.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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Old Source Packages for BioC 3.9 Source Archive