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 (3.17)

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>

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


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biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.5.0
In Bioconductor since BioC 3.14 (R-4.1) (1 year)
License GPL-3 + file LICENSE
Depends GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0)
Imports assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures
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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