{ "_id": "6a2549644b233be19839b765", "Package": "FLASHMM", "Title": "Fast and Scalable Single Cell Differential Expression Analysis\nusing Mixed-Effects Models", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Changjiang\", \"Xu\", email = \"changjiang.xu@utoronto.ca\", role = c(\"aut\", \"cre\")),\nperson(\"Delaram\", \"Pouyabahar\", email = \"d.pouyabahar@mail.utoronto.ca\", role = \"ctb\"),\nperson(\"Veronique\", \"Voisin\", email = \"veronique.voisin@gmail.com\", role = \"ctb\"),\nperson(\"Gary\", \"Bader\", email = \"gary.bader@utoronto.ca\", role = \"ctb\"))", "Description": "A fast and scalable linear mixed-effects model (LMM)\nestimation algorithm for analysis of single-cell differential\nexpression. The algorithm uses summary-level statistics and\nrequires less computer memory to fit the LMM.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/BaderLab/FLASHMM", "BugReports": "https://github.com/BaderLab/FLASHMM/issues", "Repository": "https://baderlab.r-universe.dev", "Date/Publication": "2026-04-08 03:15:49 UTC", "RemoteUrl": "https://github.com/baderlab/flashmm", "RemoteRef": "HEAD", "RemoteSha": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-07 10:31:36 UTC", "User": "root" }, "Author": "Changjiang Xu [aut, cre],\nDelaram Pouyabahar [ctb],\nVeronique Voisin [ctb],\nGary Bader [ctb]", "Maintainer": "Changjiang Xu ", "MD5sum": "73669c7cb34789f029cc486f9bc986aa", "_user": "baderlab", "_type": "src", "_file": "FLASHMM_1.3.0.tar.gz", "_fileid": "16f583512af628fd15e613b51dfac79a7fa766b350f73c69bb5d4cc6da8107e1", "_filesize": 641165, "_sha256": "16f583512af628fd15e613b51dfac79a7fa766b350f73c69bb5d4cc6da8107e1", "_created": "2026-06-07T10:31:36.000Z", "_published": "2026-06-07T10:35:16.391Z", "_distro": "noble", "_jobs": [ { "job": 79951683386, "time": 143, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7463288325" }, { "job": 79951683374, "time": 149, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7463288910" }, { "job": 79951683392, "time": 186, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7463288843" }, { "job": 79951683388, "time": 151, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7463286576" }, { "job": 79951461650, "time": 209, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7463271999" }, { "job": 79951683381, "time": 100, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7463283777" }, { "job": 79951683398, "time": 118, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7463285539" }, { "job": 79951683389, "time": 96, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7463283276" }, { "job": 79951683390, "time": 94, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7463283048" } ], "_buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/baderlab/flashmm", "_commit": { "id": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "author": "ChangjiangXu ", "committer": "ChangjiangXu ", "message": "Initial commit\n", "time": 1775618149 }, "_maintainer": { "name": "Changjiang Xu", "email": "changjiang.xu@utoronto.ca", "login": "changjiangxu", "description": "", "uuid": 15987248 }, "_registered": true, "_dependencies": [ { "package": "stats", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" } ], "_owner": "baderlab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-31", "n": 2 }, { "week": "2025-32", "n": 15 }, { "week": "2025-33", "n": 4 }, { "week": "2025-34", "n": 4 }, { "week": "2025-35", "n": 8 }, { "week": "2026-15", "n": 8 } ], "_tags": [], "_stars": 11, "_contributors": [ { "user": "changjiangxu", "count": 107, "uuid": 15987248 }, { "user": "delipouya", "count": 3, "uuid": 61254803 } ], "_userbio": { "uuid": 3812492, "type": "organization", "name": "Bader Lab, University of Toronto" }, "_downloads": { "count": 539, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FLASHMM" }, "_devurl": "https://github.com/baderlab/flashmm", "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FLASHMM.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/baderlab/flashmm", "_realowner": "baderlab", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2025-01-17" }, { "version": "1.1.0", "date": "2025-03-11" }, { "version": "1.2.0", "date": "2025-03-31" }, { "version": "1.2.1", "date": "2025-04-09" }, { "version": "1.2.2", "date": "2025-08-19" }, { "version": "1.2.3", "date": "2025-08-26" }, { "version": "1.3.0", "date": "2026-04-07" } ], "_exports": [ "contrast.matrix", "flashmm", "lmm", "lmmfit", "lmmtest", "simuRNAseq", "sslmm" ], "_help": [ { "page": "contrast.matrix", "title": "Construct Contrast Matrix", "topics": [ "contrast.matrix" ] }, { "page": "flashmm", "title": "Fitting Linear Mixed-effects Models", "topics": [ "flashmm" ] }, { "page": "lmm", "title": "Fitting Linear Mixed-effects Models", "topics": [ "lmm" ] }, { "page": "lmmfit", "title": "Fitting Linear Mixed-effects Models", "topics": [ "lmmfit" ] }, { "page": "lmmtest", "title": "Testing Fixed Effects and Contrasts of the Fixed Effects", "topics": [ "lmmtest" ] }, { "page": "simuRNAseq", "title": "Simulating Multi-sample Multi-cell-type scRNA-seq Dataset based on Negative Binomial Distribution", "topics": [ "simuRNAseq" ] }, { "page": "sslmm", "title": "Computing Summary-level Data from Individual-level Data", "topics": [ "sslmm" ] } ], "_readme": "https://github.com/baderlab/flashmm/raw/HEAD/README.md", "_rundeps": [ "lattice", "MASS", "Matrix" ], "_vignettes": [ { "source": "FLASHMM-vignette.Rmd", "filename": "FLASHMM-vignette.html", "title": "Single-cell differential expression analysis with FLASHMM", "author": "Changjiang Xu, Delaram Pouyabahar, Veronique Voisin, and Gary D. Bader", "engine": "knitr::rmarkdown", "headings": [ "FLASHMM", "Linear mixed-effects model", "The fast and scalable algorithm", "Functions", "Example", "Simulating scRNA-seq data", "DE analysis of scRNA-seq data", "LMM design", "LMM fitting", "Hypothesis testing", "Using ML method", "Methods", "LMM parameter estimation", "Remarks", "Session info", "References" ], "created": "2025-01-06 00:36:36", "modified": "2026-04-07 03:33:23", "commits": 24 } ], "_score": 5.694605198933568, "_indexed": true, "_nocasepkg": "flashmm", "_universes": [ "baderlab", "changjiangxu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-06-07T10:33:54.000Z", "distro": "noble", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "117a42e03e2675b822cf6cc6a98e6a4e94fb4e99522829d1657e1c314211b516", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-06-07T10:33:57.000Z", "distro": "noble", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "6d61c36c31c730c800b2c097f00322fc72d8ab8c59ae5922049c767c2c1433fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-06-07T10:33:58.000Z", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "ec91ca910c4b9293e464ec2965653c48070ed0e6e52f93966c6873a9d12574f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-06-07T10:33:41.000Z", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "fd87de0e49f62540aac4b74106dbee4f983ae050212b6b5e41eab0330da36816", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-06-07T10:33:36.000Z", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "987a93fbf49059bfc9e4316a9b1505869c24ee041fa05d35e4b7a8f40d629127", "status": "success", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-06-07T10:33:20.000Z", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "641f7389787670d42ed142ea63d1eec7491b58a87ffbcc998517caf6a88fc49d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-06-07T10:32:58.000Z", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "116df2da13736243770e0bef6e0ec2aaa692be42cfb479b90f27ce4ee0c45052", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-06-07T10:33:03.000Z", "commit": "3fe4db9cbfc2dc232d657c95aefddf4a0ca31fc0", "fileid": "3aeb63bc5627f80070aa8a94f975ec1e9eb537f682b53bc34e3ea01c947644f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/baderlab/actions/runs/27089910381" } ] }