svaNUMT

This is the released version of svaNUMT; for the devel version, see svaNUMT.

NUMT detection from structural variant calls

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DOI: 10.18129/B9.bioc.svaNUMT

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0003-1433-0484

Maintainer: Ruining Dong <lnyidrn at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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")

svaNUMT Package HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

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Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation

Version 1.16.0

In Bioconductor since BioC 3.14 (R-4.1) (4 years)

License GPL-3 + file LICENSE

Depends GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0)

Imports assertthat, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, pwalign

System Requirements

URL

Bug Reports https://github.com/PapenfussLab/svaNUMT/issues

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_1.16.0.tar.gz

Windows Binary (x86_64) svaNUMT_1.16.0.zip

macOS Binary (x86_64) svaNUMT_1.16.0.tgz

macOS Binary (arm64) svaNUMT_1.16.0.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/

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