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Bioconductor - svaNUMT (development version)

svaNUMT

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

NUMT detection from structural variant calls

Bioconductor version: Development (3.22)

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: 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")

# 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")
Details biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation Version 1.15.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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, pwalign System Requirements URL Bug Reports https://github.com/PapenfussLab/svaNUMT/issues See More Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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