StructuralVariantAnnotation

DOI: 10.18129/B9.bioc.StructuralVariantAnnotation    

This is the development version of StructuralVariantAnnotation; to use it, please install the devel version of Bioconductor.

Variant annotations for structural variants

Bioconductor version: Development (3.10)

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 (!requireNamespace("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")

 

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

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL-3
Depends GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 3.6.0)
Imports assertthat, Biostrings, stringr, dplyr, methods, rlang
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package StructuralVariantAnnotation_1.1.0.tar.gz
Windows Binary StructuralVariantAnnotation_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) StructuralVariantAnnotation_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/StructuralVariantAnnotation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/StructuralVariantAnnotation
Package Short Url https://bioconductor.org/packages/StructuralVariantAnnotation/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: