{ "_id": "6abda99899f7aa8c6aa50b77", "Package": "multipletR", "Type": "Package", "Title": "Adaptive Detection of Human-Mouse Multiplets in PDX Single-Cell\nData", "Version": "0.99.9", "Authors@R": "c(\nperson(\"Alexandra\", \"Gerveni\",\nemail = \"alexandra.gerveni@hotmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0004-5428-5889\")),\nperson(\"Amy\", \"Olex\", role = \"aut\"),\nperson(\"Mikhail\", \"Dozmorov\", role = c(\"aut\", \"fnd\"),\ncomment = \"P50AA022537\"),\nperson(\"Gamze\", \"Bulut\", role = \"aut\"),\nperson(\"J. Chuck\", \"Harrell\", role = \"fnd\",\ncomment = \"U54CA283762\"),\nperson(\"Jose\", \"Trevino\", role = \"fnd\",\ncomment = \"U54CA283762\"))", "Description": "Detects human-mouse multiplets in patient-derived\nxenograft (PDX) single-cell RNA-seq data using an adaptive\nthreshold method that does not assume a fixed species\nproportion. Takes a 10x CellRanger GEM classification file and\nreturns the data with added multiplet classifications, with\noptional diagnostic plots and helpers to annotate a Seurat or\nSingleCellExperiment object with multiplet classifications or\nremove multiplets from it. The adaptive approach starts from a\nconservative central region of balanced droplets and expands\nits thresholds until the selected cells no longer resemble true\nmultiplets, which handles the imbalanced species mixtures\ncommon in real PDX samples.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "biocViews": "SingleCell, RNASeq, Preprocessing, QualityControl,\nTranscriptomics, Classification", "URL": "https://github.com/Alex05a/multipletR", "BugReports": "https://github.com/Alex05a/multipletR/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-22 01:42:01 UTC", "RemoteUrl": "https://github.com/bioc/multipletR", "RemoteRef": "HEAD", "RemoteSha": "a3af58a3c95a2917fc107393129e15e811668719", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 00:18:53 UTC", "User": "root" }, "Author": "Alexandra Gerveni [aut, cre] (ORCID:\n),\nAmy Olex [aut],\nMikhail Dozmorov [aut, fnd] (P50AA022537),\nGamze Bulut [aut],\nJ. Chuck Harrell [fnd] (U54CA283762),\nJose Trevino [fnd] (U54CA283762)", "Maintainer": "Alexandra Gerveni ", "_user": "bioc", "_type": "src", "_file": "multipletR_0.99.9.tar.gz", "_fileid": "https://r2.ropensci.org/e18e6f869964b4f86758438b229b708dc49e16dc4a00f7ee205da865fb245d3e", "_filesize": 1559727, "_sha256": "e18e6f869964b4f86758438b229b708dc49e16dc4a00f7ee205da865fb245d3e", "_expires": "2027-01-09T00:30:11.000Z", "_created": "2026-10-01T00:18:53.000Z", "_published": "2026-10-01T00:30:16.264Z", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481", "_status": "success", "_upstream": "https://github.com/bioc/multipletR", "_commit": { "id": "a3af58a3c95a2917fc107393129e15e811668719", "author": "Alexandra ", "committer": "Alexandra ", "message": "Import SingleCellExperiment class so the Import is used, clearing the note; bump to 0.99.9\n", "time": 1790041321 }, "_maintainer": { "name": "Alexandra Gerveni", "email": "alexandra.gerveni@hotmail.com", "login": "alex05a", "description": "I am a Biostatistician with an MS in Biostatistics from Virginia Commonwealth University.", "uuid": 143851122, "orcid": "0009-0004-5428-5889" }, "_distro": "resolute", "_jobs": [ { "job": 110158183928, "time": 216, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11133861508" }, { "job": 110158183984, "time": 442, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11133842129" }, { "job": 110158184082, "time": 465, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11132774939" }, { "job": 110158183978, "time": 200, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11133857175" }, { "job": 110158183976, "time": 249, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11133603360" }, { "job": 110156932143, "time": 274, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11133068610" }, { "job": 110158183974, "time": 176, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11133666929" }, { "job": 110158184054, "time": 278, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11133811698" }, { "job": 110158184084, "time": 248, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11132529728" }, { "job": 110158184061, "time": 229, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11132944130" } ], "_registered": true, "_dependencies": [ { "package": "diptest", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-28", "n": 14 }, { "week": "2026-29", "n": 7 }, { "week": "2026-34", "n": 15 }, { "week": "2026-35", "n": 4 }, { "week": "2026-37", "n": 1 }, { "week": "2026-38", "n": 2 }, { "week": "2026-39", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.9", "bioc": "3.24" } ], "_topics": [ "singlecell", "rnaseq", "preprocessing", "qualitycontrol", "transcriptomics", "classification" ], "_stars": 0, "_contributors": [ { "user": "alex05a", "count": 45, "uuid": 143851122 }, { "user": "mdozmorov", "count": 3, "uuid": 864945 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 471, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/alex05a/multipletr", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/multipletR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "detect_multiplets", "remove_multiplets" ], "_help": [ { "page": "detect_multiplets", "title": "Detect human-mouse multiplets in PDX single-cell data", "topics": [ "detect_multiplets" ] }, { "page": "remove_multiplets", "title": "Annotate (and optionally remove) multiplets in a Seurat or SingleCellExperiment object", "topics": [ "remove_multiplets" ] } ], "_readme": "https://github.com/bioc/multipletR/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "diptest", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "patchwork", "R6", "RColorBrewer", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "multipletR-introduction.Rmd", "filename": "multipletR-introduction.html", "title": "Detecting human-mouse multiplets in PDX single-cell data with multipletR", "author": "Alexandra Gerveni", "engine": "knitr::rmarkdown", "headings": [ "multipletR", "The problem", "The approach", "Installation", "The input: Cell Ranger's GEM classification file", "How the data is generated", "Where to find it", "What it contains", "Why this is the input multipletR needs", "Column-name flexibility", "Detecting multiplets", "Reading the diagnostic plots", "Adjusting the thresholds", "Using the results with Seurat or SingleCellExperiment", "Functions", "How it works", "Session info" ], "created": "2026-07-11 19:02:05", "modified": "2026-09-20 21:05:14", "commits": 15 } ], "_score": 4.544068044350276, "_indexed": true, "_nocasepkg": "multipletr", "_universes": [ "bioc", "alex05a" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.9", "date": "2026-10-01T00:24:30.000Z", "distro": "resolute", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/1850f4be83987037a13993d3a2d38eb2acb2ed7dac03499c0834cd89a4c2d649", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.6.1", "os": "linux", "version": "0.99.9", "date": "2026-10-01T00:25:38.000Z", "distro": "resolute", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/70997a63e11661ed0d389b7b7044d6e21a1d7a32fc9f5520ee0c03853630cc18", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.5.3", "os": "mac", "version": "0.99.9", "date": "2026-10-01T00:24:36.000Z", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/573b47a5ef877af325f5a9696602d77fbb462661a062433dc0e6d4f555e4b261", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.6.1", "os": "mac", "version": "0.99.9", "date": "2026-10-01T00:27:27.000Z", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/bb251ca06d5dd7a463250df81516d5b677d499a63136000d1aeb3bb55318f610", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.9", "date": "2026-10-01T00:22:15.000Z", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/596985bf1f851303e838543a698d41b55716fb37f537bd209f1782281d77cef4", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.7.0", "os": "win", "version": "0.99.9", "date": "2026-10-01T00:20:57.000Z", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/264cc3d755b0ad65d18770ae055ff49470960aaa6700e61d33d0da5201cc53eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.5.3", "os": "win", "version": "0.99.9", "date": "2026-10-01T00:20:47.000Z", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/fdfa915738727f89f5484f415f7f1e58f642a7931703d30087910794d1fc0107", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" }, { "r": "4.6.1", "os": "win", "version": "0.99.9", "date": "2026-10-01T00:20:46.000Z", "commit": "a3af58a3c95a2917fc107393129e15e811668719", "fileid": "https://r2.ropensci.org/c2a02d419ad2dfa2439a7012c83fa97b5d540c71104e553fe8e8a62dd8a1d9a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36795170481" } ] }