StructuralVariantAnnotation
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see StructuralVariantAnnotation.
Variant annotations for structural variants
Bioconductor version: 3.15
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("StructuralVariantAnnotation")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation |
| Version | 1.12.0 |
| 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | StructuralVariantAnnotation_1.12.0.tar.gz |
| Windows Binary | StructuralVariantAnnotation_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | StructuralVariantAnnotation_1.12.0.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 3.15 | Source Archive |