svaNUMT

DOI: 10.18129/B9.bioc.svaNUMT    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see svaNUMT.

NUMT detection from structural variant calls

Bioconductor version: 3.14

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 "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	svaNUMT Package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	GPL-3
Depends	GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, R (>= 4.0)
Imports	assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures
LinkingTo
Suggests	TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, plyranges, circlize, tictoc, IRanges, SummarizedExperiment, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/PapenfussLab/svaNUMT/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	svaNUMT_1.0.0.tar.gz
Windows Binary	svaNUMT_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	svaNUMT_1.0.0.tgz
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