{ "_id": "6a1b10ca1d7bb097a0a0b7b5", "Package": "scConform", "Type": "Package", "Title": "Conformal Inference for Cell Type Annotation", "Version": "1.0.0", "Authors@R": "c(\nperson(\"Daniela\", \"Corbetta\",\nemail = \"daniela.corbetta@unipd.it\",\nrole = c(\"aut\", \"cre\"),\ncomment=c(ORCID=\"0009-0008-5026-8271\")),\nperson(\"Tram\", \"Nguyen\", role = \"ctb\"),\nperson(\"Nitesh\", \"Turaga\", role = \"ctb\"),\nperson(\"Ludwig\", \"Geistlinger\", role = \"ctb\")\n)", "Description": "Builds prediction interval for cell type annotation using\nconformal inference and conformal risk control. It provides two\nmain methods. The first one gives prediction intervals with\ncoverage guarantees based on standard conformal inference. The\nsecond one instead gives hierarchical prediction intervals that\nare consistent with the cell ontology.", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "biocViews": "Software, Classification, SingleCell, Annotation", "URL": "https://github.com/ccb-hms/scConform", "BugReports": "https://github.com/ccb-hms/scConform/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:06:42 UTC", "RemoteUrl": "https://github.com/bioc/scConform", "RemoteRef": "RELEASE_3_23", "RemoteSha": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 11:05:11 UTC", "User": "root" }, "Author": "Daniela Corbetta [aut, cre] (ORCID:\n),\nTram Nguyen [ctb],\nNitesh Turaga [ctb],\nLudwig Geistlinger [ctb]", "Maintainer": "Daniela Corbetta ", "MD5sum": "bdf9635b8b89d3b3aa92b26141773bda", "_user": "bioc-release", "_type": "src", "_file": "scConform_1.0.0.tar.gz", "_fileid": "184e5ba1051e6bc3dc47d8a67080ff28a5cd4437a20f96ea102c7bf874de5b14", "_filesize": 769053, "_sha256": "184e5ba1051e6bc3dc47d8a67080ff28a5cd4437a20f96ea102c7bf874de5b14", "_created": "2026-05-30T11:05:11.000Z", "_published": "2026-05-30T16:31:06.114Z", "_jobs": [ { "job": 78644509748, "time": 212, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307809738" }, { "job": 78644509742, "time": 374, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307823916" }, { "job": 78644509741, "time": 357, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307821994" }, { "job": 78644509770, "time": 149, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7309641832" }, { "job": 78644509765, "time": 176, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7309644232" }, { "job": 78643854356, "time": 520, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307727252" }, { "job": 78644509749, "time": 189, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307808180" }, { "job": 78644509771, "time": 1501, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307923259" }, { "job": 78644509766, "time": 1272, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307903110" }, { "job": 78644509768, "time": 1087, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307886202" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scConform", "_commit": { "id": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381602 }, "_maintainer": { "name": "Daniela Corbetta", "email": "daniela.corbetta@unipd.it" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "igraph", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "Rgraphviz", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "VGAM", "role": "Suggests" }, { "package": "ontoProc", "role": "Suggests" }, { "package": "MerfishData", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" }, { "package": "scuttle", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "scran", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-51", "n": 1 }, { "week": "2026-04", "n": 2 }, { "week": "2026-06", "n": 2 }, { "week": "2026-07", "n": 4 }, { "week": "2026-10", "n": 7 }, { "week": "2026-12", "n": 3 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.0", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "software", "classification", "singlecell", "annotation", "u24ca289073" ], "_stars": 7, "_contributors": [ { "user": "danielacorbetta", "count": 99, "uuid": 81688280 }, { "user": "tram-nguyen-n", "count": 9, "uuid": 150388074 }, { "user": "lgeistlinger", "count": 1, "uuid": 11871050 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 242, "source": "https://www.bioconductor.org/packages/stats/bioc/scConform" }, "_devurl": "https://github.com/ccb-hms/scconform", "_rbuild": "4.6.0", "_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/scConform.html", "manual.pdf" ], "_homeurl": "https://github.com/ccb-hms/scconform", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getCommonAncestor", "getPredictionSets", "plotResult" ], "_help": [ { "page": "getCommonAncestor", "title": "Return the common ancestor of the labels in the prediction set", "topics": [ "getCommonAncestor" ] }, { "page": "getPredictionSets", "title": "Get conformal prediction sets", "topics": [ "getPredictionSets" ] }, { "page": "plotResult", "title": "Plot prediction sets", "topics": [ "plotResult" ] } ], "_readme": "https://github.com/bioc/scConform/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "cli", "codetools", "cpp11", "DelayedArray", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "glue", "graph", "igraph", "IRanges", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pkgconfig", "Rgraphviz", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "vctrs", "XVector" ], "_vignettes": [ { "source": "scConform.Rmd", "filename": "scConform.html", "title": "Conformal Prediction for cell type annotation", "author": "Daniela Corbetta", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Preliminaries", "Setup", "Load data and cell ontology", "Build the ontology", "Preprocess data", "Fit a classification model", "Method 1: standard conformal inference", "Algorithm", "Obtain prediction matrices", "Obtain conformal prediction sets", "Method 2: exploit the cell ontology", "Obtain hierarchical prediction sets", "Visualization", "R.session Info" ], "created": "2024-06-17 20:38:47", "modified": "2026-03-20 15:27:19", "commits": 5 } ], "_score": 5.690196080028514, "_indexed": false, "_nocasepkg": "scconform", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/scConform", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-30T11:21:55.000Z", "distro": "noble", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "85119860a65e8648e69b2536f56e4f37c9d1661c8527913d8b97ff2e97b5172b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-30T11:21:39.000Z", "distro": "noble", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "17c2a1986b1e6a309c9ee142715cd843b46305106a87f1eaec93ba9ba0a9b363", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-30T16:29:17.000Z", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "ec4983af98efa0dc5212eaf8d9602fab42358a57ffb7f2cb6fa98921316fc75f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-30T16:29:20.000Z", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "0fc40fdfe23ff060f2b502c6365b859a3370e5f7027253a52a2128c497e4fbbc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-30T11:20:53.000Z", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "30e44b929d25e97574bfdfaa9c8ab70a9558ee1e736bfb0ca8f5b5cc5bb377f1", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-30T11:40:33.000Z", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "a99922941e33536cfb8d37118deaf15bcfffbb631790cbdeb05821c356d203e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-30T11:36:45.000Z", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "4e311cd867e70b2e59b766b8896cc5f918994eeedf165420f1fed7e68dc86c4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-30T11:33:23.000Z", "commit": "11ab49c329067bb73443d6afa7fbd73518b7bcf8", "fileid": "66688caaa6cff320c86df4a6c9cb5a2d6ccf6db6202118f4e7e0731093945b1d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681047380" } ] }