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


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

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
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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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive