svaNUMT
This is the development version of svaNUMT; for the stable release version, see svaNUMT.
NUMT detection from structural variant calls
Bioconductor version: Development (3.21)
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.
Author: Ruining Dong [aut, cre] (ORCID:
Maintainer: Ruining Dong <lnyidrn at gmail.com>
citation("svaNUMT")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("svaNUMT")
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("svaNUMT")| svaNUMT Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | GPL-3 + file LICENSE |
| Depends | GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) |
| Imports | assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures, pwalign |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/PapenfussLab/svaNUMT/issues |
See More
| Suggests | TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown |
| 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 | svaNUMT_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/svaNUMT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/svaNUMT |
| Bioc Package Browser | https://code.bioconductor.org/browse/svaNUMT/ |
| Package Short Url | https://bioconductor.org/packages/svaNUMT/ |
| Package Downloads Report | Download Stats |