svaNUMT
This is thereleased version of svaNUMT; for the devel version, seesvaNUMT.
NUMT detection from structural variant calls
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: 0000-0003-1433-0484
Maintainer: Ruining Dong <lnyidrn at gmail.com>
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 appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 + fileLICENSE |
| 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 |
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
FollowInstallation 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/ |
| Package Downloads Report | Download Stats |