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svaNUMT

This is the development version of svaNUMT; for the stable release version, see svaNUMT.

NUMT detection from structural variant calls


Bioconductor version: Development (3.19)

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]

Maintainer: Ruining Dong <lnyidrn at gmail.com>

Citation (from within R, enter citation("svaNUMT")):

Installation

To install this package, start R (version "4.4") 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 PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package svaNUMT_1.9.0.tar.gz
Windows Binary svaNUMT_1.9.0.zip
macOS Binary (x86_64) svaNUMT_1.9.0.tgz
macOS Binary (arm64) svaNUMT_1.9.0.tgz
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