{ "_id": "6ad92a0f992ad85420b5f508", "Package": "STRprofilerR", "Title": "Compare Short Tandem Repeat Profiles for Model Authentication", "Version": "0.99.1", "Authors@R": "person(\"Jared\", \"Andrews\", email = \"jared.andrews07@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0780-6248\"))", "Description": "Compares short tandem repeat (STR) profiles to\nauthenticate biomedical models such as cell lines and\nxenografts against the primary tissue samples they were derived\nfrom. Provides the Tanabe (Sorenson-Dice), Masters (versus\nquery), and Masters (versus reference) similarity scores,\nheuristics for detecting sample mixing, flexible ingest of wide\nand long profile formats, comparison against user-supplied\nreference databases, and querying of the Cellosaurus knowledge\nbase through the CLASTR REST API. A command line application is\nincluded for use in automated workflows, and a Shiny\napplication for interactive queries.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/j-andrews7/STRprofilerR", "BugReports": "https://github.com/j-andrews7/STRprofilerR/issues", "biocViews": "Software, QualityControl, Genetics, CellBasedAssays", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-13 19:01:19 UTC", "RemoteUrl": "https://github.com/bioc/STRprofilerR", "RemoteRef": "HEAD", "RemoteSha": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-21 21:01:24 UTC", "User": "root" }, "Author": "Jared Andrews [aut, cre] (ORCID:\n)", "Maintainer": "Jared Andrews ", "_user": "bioc", "_type": "src", "_file": "STRprofilerR_0.99.1.tar.gz", "_fileid": "https://r2.ropensci.org/3216e20a647487d937e0740a79288756f0b2371831ebf76c70d535846e2b7505", "_filesize": 580139, "_sha256": "3216e20a647487d937e0740a79288756f0b2371831ebf76c70d535846e2b7505", "_expires": "2027-01-29T21:09:33.000Z", "_created": "2026-10-21T21:01:24.000Z", "_published": "2026-10-21T21:09:35.214Z", "_upstream": "https://github.com/bioc/STRprofilerR", "_status": "success", "_maintainer": { "name": "Jared Andrews", "email": "jared.andrews07@gmail.com", "login": "j-andrews7", "description": "Senior Bioinformatics Research Scientist at St. Jude Children's Research Hospital", "uuid": 10225716, "orcid": "0000-0002-0780-6248" }, "_jobs": [ { "job": 119483753299, "time": 354, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12382800776" }, { "job": 119483753281, "time": 252, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12380869707" }, { "job": 119483753521, "time": 449, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12382771743" }, { "job": 119483753272, "time": 149, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12381427799" }, { "job": 119483753397, "time": 166, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12381716489" }, { "job": 119480998478, "time": 334, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12382120693" }, { "job": 119483753333, "time": 274, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12381452533" }, { "job": 119483753661, "time": 156, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12382125993" }, { "job": 119483753364, "time": 155, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12381466453" }, { "job": 119483753396, "time": 333, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12382286571" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636", "_commit": { "id": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "author": "Jared Andrews ", "committer": "Jared Andrews ", "message": "version bump\n", "time": 1791918079 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "httr2", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "bslib", "version": ">= 0.7.0", "role": "Suggests" }, { "package": "curl", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "htmlwidgets", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "Rapp", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shiny", "version": ">= 1.8.1", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "writexl", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-38", "n": 2 }, { "week": "2026-39", "n": 11 }, { "week": "2026-42", "n": 2 } ], "_tags": [], "_topics": [ "software", "qualitycontrol", "genetics", "cellbasedassays", "cell-line-authentication", "model-authentication", "omnistr", "powerplex", "str-profiling", "xenograft-authentication" ], "_stars": 0, "_contributors": [ { "user": "j-andrews7", "count": 15, "uuid": 10225716 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/j-andrews7/strprofilerr", "_searchresults": 7, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/STRprofilerR.html", "LICENSE" ], "_cranurl": false, "_exports": [ "alleles", "alleles<-", "amelogeninMarkers", "as.data.frame", "classifyMarkers", "clastrBatchQuery", "clastrMarkers", "clastrQuery", "cleanAlleles", "compareProfiles", "flagMixedSamples", "harmonizeMarkers", "markerAliases", "markerData", "markerData<-", "markers", "params", "provenance", "queryProfiles", "readSTRProfiles", "referenceProfiles", "sampleData", "sampleData<-", "scoreProfiles", "scoreQuery", "scores", "show", "strHTMLTable", "STRprofilerApp", "STRProfiles", "summarizeMatches", "summary", "validateClastrMarkers", "writeSTRProfiles", "writeSTRResults" ], "_datasets": [ { "name": "pdxSTRProfiles", "title": "STR profiles of patient-derived models from JAX and the NCI PDMR", "object": "pdxSTRProfiles", "file": "pdxSTRProfiles.rda", "class": [ "STRProfiles" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "STRProfiles-accessors", "title": "Accessors for STRProfiles objects", "topics": [ "alleles", "alleles,STRProfiles-method", "alleles<-", "alleles<-,STRProfiles-method", "markerData", "markerData,STRProfiles-method", "markerData<-", "markerData<-,STRProfiles-method", "markers", "markers,STRProfiles-method", "provenance", "provenance,STRProfiles-method", "sampleData", "sampleData,STRProfiles-method", "sampleData<-", "sampleData<-,STRProfiles-method", "STRProfiles-accessors" ] }, { "page": "amelogeninMarkers", "title": "Recognised amelogenin marker names", "topics": [ "amelogeninMarkers" ] }, { "page": "classifyMarkers", "title": "Classify STR markers", "topics": [ "classifyMarkers" ] }, { "page": "clastrBatchQuery", "title": "Query CLASTR in batch and save the XLSX result", "topics": [ "clastrBatchQuery" ] }, { "page": "clastrMarkers", "title": "Marker names accepted by the CLASTR API", "topics": [ "clastrMarkers", "validateClastrMarkers" ] }, { "page": "clastrQuery", "title": "Query the Cellosaurus knowledge base via CLASTR", "topics": [ "clastrQuery" ] }, { "page": "cleanAlleles", "title": "Clean and split a vector of allele calls", "topics": [ "cleanAlleles" ] }, { "page": "compareProfiles", "title": "Compare STR profiles end to end", "topics": [ "compareProfiles" ] }, { "page": "flagMixedSamples", "title": "Flag potentially mixed samples", "topics": [ "flagMixedSamples" ] }, { "page": "markerAliases", "title": "Marker name harmonisation", "topics": [ "harmonizeMarkers", "markerAliases" ] }, { "page": "pdxSTRProfiles", "title": "STR profiles of patient-derived models from JAX and the NCI PDMR", "topics": [ "pdxSTRProfiles" ] }, { "page": "readSTRProfiles", "title": "Read STR profiles from file", "topics": [ "readSTRProfiles" ] }, { "page": "scoreProfiles", "title": "Score STR profiles against each other", "topics": [ "scoreProfiles" ] }, { "page": "scoreQuery", "title": "Score a single profile against a reference set", "topics": [ "scoreQuery" ] }, { "page": "STRComparison-accessors", "title": "Accessors for STRComparison objects", "topics": [ "params", "params,STRComparison-method", "queryProfiles", "queryProfiles,STRComparison-method", "referenceProfiles", "referenceProfiles,STRComparison-method", "scores", "scores,STRComparison-method", "show,STRComparison-method", "STRComparison-accessors", "summary,STRComparison-method" ] }, { "page": "STRComparison-class", "title": "STRComparison: the result of comparing STR profiles", "topics": [ "STRComparison", "STRComparison-class" ] }, { "page": "strHTMLTable", "title": "Write a data frame as a standalone HTML table", "topics": [ "strHTMLTable" ] }, { "page": "STRprofilerApp", "title": "Launch the STRprofiler Shiny application", "topics": [ "STRprofilerApp" ] }, { "page": "STRProfiles", "title": "Build STRProfiles from a data.frame", "topics": [ "STRProfiles" ] }, { "page": "STRProfiles-class", "title": "STRProfiles: a set of short tandem repeat profiles", "topics": [ "STRProfiles-class" ] }, { "page": "STRProfiles-methods", "title": "Dimensions, subsetting, and coercion for STRProfiles", "topics": [ "$,STRProfiles-method", "as.data.frame,STRProfiles-method", "c,STRProfiles-method", "dim,STRProfiles-method", "dimnames,STRProfiles-method", "show,STRProfiles-method", "STRProfiles-methods", "[,STRProfiles,ANY,ANY,ANY-method", "[,STRProfiles-method" ] }, { "page": "summarizeMatches", "title": "Summarise pairwise scores into one row per query", "topics": [ "summarizeMatches" ] }, { "page": "writeSTRProfiles", "title": "Write STR profiles to file", "topics": [ "writeSTRProfiles" ] }, { "page": "writeSTRResults", "title": "Write comparison results to disk", "topics": [ "writeSTRResults" ] } ], "_pkglogo": "https://github.com/bioc/STRprofilerR/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/STRprofilerR/raw/HEAD/README.md", "_rundeps": [ "askpass", "BiocGenerics", "cli", "curl", "generics", "glue", "httr2", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "openssl", "R6", "rlang", "S4Vectors", "sys", "vctrs", "withr" ], "_vignettes": [ { "source": "STRprofilerR.Rmd", "filename": "STRprofilerR.html", "title": "Comparing STR profiles with STRprofilerR", "author": "Jared Andrews", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Reading profiles", "Alleles are stored pre-split", "Marker names", "Metadata", "Scoring", "Comparing end to end", "Mixing", "Writing results", "Querying Cellosaurus", "The command line application", "The Shiny application", "STRprofilerR in a larger workflow", "Bioconductor data structures", "The bundled PDX database", "Generating profiles from raw data", "Carrying authentication info with an experiment", "Maintaining a reference database", "Session info" ], "created": "2026-09-15 22:55:50", "modified": "2026-10-13 18:57:16", "commits": 7 } ], "_score": 3.1760912590556813, "_indexed": true, "_nocasepkg": "strprofilerr", "_universes": [ "bioc", "j-andrews7" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-10-21T21:04:37.000Z", "distro": "resolute", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/433d684975b067c2f21ec481ec9e6aa9ae929983f2989389aa87d1c69316b6b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.6.1", "os": "linux", "version": "0.99.1", "date": "2026-10-21T21:07:54.000Z", "distro": "resolute", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/88f2356c48ba2531ed701ee9867a2355f5df47938f745f3f9d78d2921b0998b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-10-21T21:06:48.000Z", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/f7c88aa6d69a1ed9e4d21bb2d707d6f88f348431c0a413d569b125faeae547a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.6.1", "os": "mac", "version": "0.99.1", "date": "2026-10-21T21:04:46.000Z", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/f49af49c661ac0ac59a538497a8f010bf4863c3159c6a5b61359682314a287b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.1", "date": "2026-10-21T21:06:20.000Z", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/adc935c68b95447373337aa4dd662cf795c079281de8520a23ab372fb08469ca", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-10-21T21:02:47.000Z", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/7a405f0124b35705de1d15739da8415f3b4d9b06b04d0849c46545db10185da8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.5.3", "os": "win", "version": "0.99.1", "date": "2026-10-21T21:02:47.000Z", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/3f347b3d606f856459782213e93e95096093e347ff148f2971d63f1aa92d0a9e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" }, { "r": "4.6.1", "os": "win", "version": "0.99.1", "date": "2026-10-21T21:05:58.000Z", "commit": "fa9daea6b9345f4b25549c31fc8ec0e3c28eb8f7", "fileid": "https://r2.ropensci.org/e5247f06730222d99db20da81cb24c66dc23bde0ef564e8bf7e2d2d51692e894", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674554636" } ] }