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("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 | ||
| 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 | |
| URL |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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_1.0.0.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 |