svaNUMT
NUMT detection from structural variant calls
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("svaNUMT")Details
| Maintainer | Ruining Dong <lnyidrn@gmail.com> |
| Author | Ruining Dong [aut, cre] (ORCID: <https://orcid.org/0000-0003-1433-0484>) |
| License | GPL-3 + file LICENSE |
| Bug Reports | https://github.com/PapenfussLab/svaNUMT/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation |
| Package Short Url | https://bioconductor.org/packages/svaNUMT/ |
Citation
From within R, enter citation("svaNUMT"):
Ruining Dong. svaNUMT: NUMT detection from structural variant calls. doi:10.18129/B9.bioc.svaNUMT, R package version 1.18.0, https://bioconductor.org/packages/svaNUMT.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | svaNUMT_1.18.0.tar.gz |
| Windows binary (x86_64) | svaNUMT_1.18.0.zip |
| macOS binary (arm64) | svaNUMT_1.18.0.tgz |
| macOS binary (x86_64) | svaNUMT_1.18.0.tgz |
Dependencies
Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0)
Imports: assertthat, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, pwalign
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown