StructuralVariantAnnotation
This is the development version of StructuralVariantAnnotation; for the stable release version, see StructuralVariantAnnotation.
Variant annotations for structural variants
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Structural Variant Annotation Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) |
| Imports | assertthat, Biostrings, pwalign, 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 | shiny.gosling |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | StructuralVariantAnnotation_1.29.0.tar.gz |
| Windows Binary (x86_64) | StructuralVariantAnnotation_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | StructuralVariantAnnotation_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | StructuralVariantAnnotation_1.29.0.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 |