{ "_id": "6a49433b18cdde069385ea70", "Package": "svaNUMT", "Type": "Package", "Title": "NUMT detection from structural variant calls", "Version": "1.19.0", "Date": "2025-07-22", "Authors@R": "c(\nperson(\"Ruining\", \"Dong\", email=\"lnyidrn@gmail.com\", role=c(\"aut\", \"cre\"), comment=c(ORCID = \"0000-0003-1433-0484\")))", "Description": "svaNUMT contains functions for detecting NUMT events from\nstructural variant calls. It takes structural variant calls in\nGRanges of breakend notation and identifies NUMTs by\nnuclear-mitochondrial breakend junctions. The main function\nreports candidate NUMTs if there is a pair of valid insertion\nsites found on the nuclear genome within a certain distance\nthreshold. The candidate NUMTs are reported by events.", "License": "GPL-3 + file LICENSE", "RoxygenNote": "7.1.2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "DataImport, Sequencing, Annotation, Genetics,\nVariantAnnotation", "BugReports": "https://github.com/PapenfussLab/svaNUMT/issues", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:28 UTC", "RemoteUrl": "https://github.com/bioc/svaNUMT", "RemoteRef": "HEAD", "RemoteSha": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 12:06:48 UTC", "User": "root" }, "Author": "Ruining Dong [aut, cre] (ORCID:\n)", "Maintainer": "Ruining Dong ", "_user": "bioc", "_type": "src", "_file": "svaNUMT_1.19.0.tar.gz", "_fileid": "https://r2.ropensci.org/0edd2bdba206612c3037f94a5878aef8b5008540deac80bdb36077634868cfd2", "_filesize": 639134, "_sha256": "0edd2bdba206612c3037f94a5878aef8b5008540deac80bdb36077634868cfd2", "_expires": "2026-10-12T17:30:33.000Z", "_created": "2026-07-04T12:06:48.000Z", "_published": "2026-07-04T17:30:35.381Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615", "_status": "success", "_upstream": "https://github.com/bioc/svaNUMT", "_commit": { "id": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380988 }, "_maintainer": { "name": "Ruining Dong", "email": "lnyidrn@gmail.com", "login": "jackieduckie", "orcid": "0000-0003-1433-0484", "description": "Semi-professional dog patter", "uuid": 13995001 }, "_distro": "resolute", "_jobs": [ { "job": 85152383240, "time": 314, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8081569199" }, { "job": 85152383390, "time": 509, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8081589752" }, { "job": 85152383481, "time": 551, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8081594037" }, { "job": 85152383310, "time": 299, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8081567408" }, { "job": 85152383378, "time": 260, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8081562863" }, { "job": 85152383086, "time": 383, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8081532181" }, { "job": 85152383399, "time": 283, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8081565648" }, { "job": 85152383393, "time": 380, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8081575995" }, { "job": 85152383466, "time": 388, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8081577018" }, { "job": 85152383354, "time": 395, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8081577600" } ], "_registered": true, "_dependencies": [ { "package": "GenomicRanges", "role": "Depends" }, { "package": "rtracklayer", "role": "Depends" }, { "package": "VariantAnnotation", "role": "Depends" }, { "package": "StructuralVariantAnnotation", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "assertthat", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "plyranges", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "dataimport", "sequencing", "annotation", "genetics", "variantannotation" ], "_stars": 3, "_contributors": [ { "user": "jackieduckie", "count": 117, "uuid": 13995001 }, { "user": "d-cameron", "count": 94, "uuid": 6036536 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "jbedo", "count": 5, "uuid": 372912 }, { "user": "cbrueffer", "count": 3, "uuid": 2705287 }, { "user": "papenfuss", "count": 2, "uuid": 878100 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/papenfusslab/svanumt", "_searchresults": 9, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/svaNUMT.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/papenfusslab/svanumt", "_realowner": "bioc", "_cranurl": false, "_exports": [ "numtDetect" ], "_help": [ { "page": "numtDetect", "title": "Detecting nuclear mitochondria fusion events.", "topics": [ "numtDetect" ] }, { "page": "svaNUMT", "title": "svaNUMT: a package for NUMT detection", "topics": [ "svaNUMT" ] } ], "_readme": "https://github.com/bioc/svaNUMT/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "assertthat", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "dplyr", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "pwalign", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "StructuralVariantAnnotation", "SummarizedExperiment", "sys", "tibble", "tidyselect", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "svaNUMT.Rmd", "filename": "svaNUMT.html", "title": "svaNUMT Quick Overview", "author": "Ruining Dong", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Using GRanges for structural variants: a breakend-centric data structure", "Workflow", "Loading data from VCF", "Identifying Nuclear-mitochondrial Genome Fusion Events", "Visualising breakpoint pairs via circos plots", "SessionInfo" ], "created": "2021-07-21 04:21:33", "modified": "2025-07-22 19:33:49", "commits": 4 } ], "_score": 5.352182518111363, "_indexed": true, "_nocasepkg": "svanumt", "_universes": [ "bioc", "jackieduckie", "papenfusslab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-07-04T12:12:10.000Z", "distro": "resolute", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/0e5b01c4e3240743b09087d2cc2c8f228f5d201dc4275b9cd1f45491c35c0104", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.6.1", "os": "linux", "version": "1.19.0", "date": "2026-07-04T12:12:48.000Z", "distro": "resolute", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/eb937dd80115a9045a4685456b3c949ea8579eb1b18b656061e95c70c865ee98", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-07-04T12:09:58.000Z", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/b1fe4a1b7bd60d2c94476487fdcb02c0ee9e9f4b9d37153f32f97b46300de704", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.6.1", "os": "mac", "version": "1.19.0", "date": "2026-07-04T12:09:33.000Z", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/64290940bb98cc62dd93ccea3864f42fdf7d9a522187f34dbeae2eca71b425b0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-07-04T12:12:10.000Z", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/21f8fa21fbe95eba5a632002a339d3ee5000c5616fc59cba4c4e98286eb40138", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-07-04T12:09:56.000Z", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/1027cfdb95ca7cee2288279956f5a01c15db224fa56875b8c1a77bf652b8ec3c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-07-04T12:09:46.000Z", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/9065f5ae2bd6b62842b2b8dc28c060e820e0c1822cdcbe2dab0dfd22ab81cd1f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" }, { "r": "4.6.1", "os": "win", "version": "1.19.0", "date": "2026-07-04T12:10:11.000Z", "commit": "66c92cc7b19008e4b62dd28dd4dab9079355463b", "fileid": "https://r2.ropensci.org/5aafe0807e6e0d0cf98ae247af53c3da1829c983f7fda36d06d0c3878d5cd8ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28705539615" } ] }