svaNUMT

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see svaNUMT.

NUMT detection from structural variant calls

Bioconductor version: 3.18

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 "4.3") 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

Need some help? Ask on the Bioconductor Support site!

Details

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

Version 1.8.0

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

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_1.8.0.tar.gz

Windows Binary svaNUMT_1.8.0.zip

macOS Binary (x86_64) svaNUMT_1.8.0.tgz

macOS Binary (arm64) svaNUMT_1.8.0.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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