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 (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.1.0
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) svaNUMT_1.1.0.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

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