{ "_id": "6aae6ed33d719c1f8407cb97", "Package": "scReClassify", "Type": "Package", "Title": "scReClassify: post hoc cell type classification of single-cell\nRNA-seq data", "Version": "1.19.0", "Authors@R": "c(\nperson(\"Pengyi\", \"Yang\", email = \"pengyi.yang@sydney.edu.au\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-1098-3138\")),\nperson(\"Taiyun\", \"Kim\", email = \"taiyun.kim91@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5028-836X\")))", "Description": "A post hoc cell type classification tool to fine-tune cell\ntype annotations generated by any cell type classification\nprocedure with semi-supervised learning algorithm AdaSampling\ntechnique. The current version of scReClassify supports Support\nVector Machine and Random Forest as a base classifier.", "License": "GPL-3 + file LICENSE", "BugReports": "https://github.com/SydneyBioX/scReClassify/issues", "URL": "https://github.com/SydneyBioX/scReClassify,\nhttp://www.bioconductor.org/packages/release/bioc/html/scReClassify.html", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.2.1", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "biocViews": "Software, Transcriptomics, SingleCell, Classification,\nSupportVectorMachine", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:54 UTC", "RemoteUrl": "https://github.com/bioc/scReClassify", "RemoteRef": "HEAD", "RemoteSha": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-19 11:08:48 UTC", "User": "root" }, "Author": "Pengyi Yang [aut] (ORCID: ),\nTaiyun Kim [aut, cre] (ORCID: )", "Maintainer": "Taiyun Kim ", "_user": "bioc", "_type": "src", "_file": "scReClassify_1.19.0.tar.gz", "_fileid": "https://r2.ropensci.org/b0a80756dc6924d7071404279ef79840b8629ff6536c2cb3df8e00f0267d7dde", "_filesize": 2488639, "_sha256": "b0a80756dc6924d7071404279ef79840b8629ff6536c2cb3df8e00f0267d7dde", "_expires": "2026-12-28T11:15:29.000Z", "_created": "2026-09-19T11:08:48.000Z", "_published": "2026-09-19T11:15:31.183Z", "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089", "_status": "success", "_upstream": "https://github.com/bioc/scReClassify", "_commit": { "id": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381014 }, "_maintainer": { "name": "Taiyun Kim", "email": "taiyun.kim91@gmail.com", "login": "taiyunkim", "description": "Data Scientist", "uuid": 32530182, "orcid": "0000-0002-5028-836X" }, "_distro": "resolute", "_jobs": [ { "job": 105887316054, "time": 172, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "10583014210" }, { "job": 105887316117, "time": 343, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10583157764" }, { "job": 105887316056, "time": 287, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10583457245" }, { "job": 105887316146, "time": 200, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10583067599" }, { "job": 105887316080, "time": 201, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10582699581" }, { "job": 105886699116, "time": 313, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10582454565" }, { "job": 105887316060, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10583213916" }, { "job": 105887316208, "time": 193, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10582969274" }, { "job": 105887316105, "time": 199, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10582509870" }, { "job": 105887316074, "time": 178, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10582399941" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "randomForest", "role": "Imports" }, { "package": "e1071", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "mclust", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "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": [ "software", "transcriptomics", "singlecell", "classification", "supportvectormachine" ], "_stars": 11, "_contributors": [ { "user": "taiyunkim", "count": 14, "uuid": 32530182 }, { "user": "pengyiyang", "count": 1, "uuid": 90130745 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 408, "source": "https://www.bioconductor.org/packages/stats/bioc/scReClassify" }, "_mentions": 2, "_devurl": "https://github.com/sydneybiox/screclassify", "_searchresults": 17, "_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/scReClassify.html", "LICENSE" ], "_homeurl": "https://github.com/sydneybiox/screclassify", "_realowner": "bioc", "_cranurl": false, "_exports": [ "bAccuracy", "matPCs", "multiAdaSampling" ], "_datasets": [ { "name": "gse87795_subset_sce", "title": "GSE827795 subset data", "object": "gse87795_subset_sce", "file": "gse87795_subset_sce.rda", "class": [ "SingleCellExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "bAccuracy", "title": "bAccuracy", "topics": [ "bAccuracy" ] }, { "page": "gse87795_subset_sce", "title": "GSE827795 subset data", "topics": [ "gse87795_subset_sce" ] }, { "page": "matPCs", "title": "matPCs function", "topics": [ "matPCs" ] }, { "page": "multiAdaSampling", "title": "multi Adaptive Sampling function", "topics": [ "multiAdaSampling" ] }, { "page": "scReClassify", "title": "scReClassify: a package for post hoc cell type classification of single-cell RNA-sequencing data.", "topics": [ "scReClassify" ] } ], "_readme": "https://github.com/bioc/scReClassify/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "class", "DelayedArray", "e1071", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "proxy", "randomForest", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "scReClassify.Rmd", "filename": "scReClassify.html", "title": "An introduction to scReClassify package", "author": "Taiyun Kim", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Loading packages and data", "Part A. scReClassify (Demonstration with synthetic mislabels)", "Dimension reduction", "Synthetic noise (Demonstration purpose)", "Use scReClassify to correct mislabeled cell types.", "Benchmark evaluation", "Part B. scReClassify (mislabeled cell type correction)", "SessionInfo" ], "created": "2021-08-26 03:27:19", "modified": "2021-09-27 04:45:20", "commits": 4 } ], "_score": 5.748962861256162, "_indexed": true, "_nocasepkg": "screclassify", "_universes": [ "bioc", "taiyunkim", "sydneybiox" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-09-19T11:13:01.000Z", "distro": "resolute", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/c6cf358b20f5582e68c97b2329a3dff82b67c9c3b851c012c4201643d2ee8bd3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.6.1", "os": "linux", "version": "1.19.0", "date": "2026-09-19T11:12:05.000Z", "distro": "resolute", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/6f3f52801fb5d11bceec27e4552eb75657f3ef0394c374b34711926981eabedc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-09-19T11:10:55.000Z", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/2ec86b888a468accecc55975611ad56bec575046d8c99776a7c62880cecc5046", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.6.1", "os": "mac", "version": "1.19.0", "date": "2026-09-19T11:11:02.000Z", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/71afaa8fcdcd9e28345c66b1d01b36629d8ebd6bf0cbbdce3e27d9641667fadf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-09-19T11:11:27.000Z", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/23912dc7a4849f6fa6a4dfe65697d2b92ae0d563773288714ec561e1be8b9c99", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-09-19T11:10:21.000Z", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/c4ba7cd853a1db5edbe9e6ff24cc9964b9ea85968f983ebf54ac7a57f5a377e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-09-19T11:10:33.000Z", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/02277b2b8d488aab9fe141402803959e8284180cb3fa03beafac7c2b05a2e4e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" }, { "r": "4.6.1", "os": "win", "version": "1.19.0", "date": "2026-09-19T11:10:15.000Z", "commit": "08344c472dac4ed9483bdeb0d0b50ebd445cea3b", "fileid": "https://r2.ropensci.org/0c571c774a073107b28a844df5631e6449f8b17efb9f315cdbf1320d8ab464b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35439080089" } ] }