StructuralVariantAnnotation
Variant annotations for structural variants
Bioconductor version: 3.23 · Package version: 1.28.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("StructuralVariantAnnotation")Details
| Maintainer | Daniel Cameron <daniel.l.cameron@gmail.com> |
| Author | Daniel Cameron [aut, cre] (ORCID: <https://orcid.org/0000-0002-0951-7116>), Ruining Dong [aut] (ORCID: <https://orcid.org/0000-0003-1433-0484>) |
| License | GPL-3 + file LICENSE |
| Downloads rank | 623 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | StructuralVariantAnnotation_1.28.0.tar.gz |
| Windows binary (x86_64) | StructuralVariantAnnotation_1.28.0.zip |
| macOS binary (arm64) | StructuralVariantAnnotation_1.28.0.tgz |
| macOS binary (x86_64) | StructuralVariantAnnotation_1.28.0.tgz |
Dependencies
Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0)
Imports: assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb
Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19