svaNUMT

DOI: 10.18129/B9.bioc.svaNUMT    

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

NUMT detection from structural variant calls

Bioconductor version: Development (3.17)

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>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version	1.5.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL-3 + file LICENSE
Depends	GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0)
Imports	assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures
LinkingTo
Suggests	TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/PapenfussLab/svaNUMT/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
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
Package Short Url	https://bioconductor.org/packages/svaNUMT/
Package Downloads Report	Download Stats