{
  "_id": "6a4f5ead21b18e15485013dd",
  "Encoding": "UTF-8",
  "Type": "Package",
  "Package": "fastglmpca",
  "Version": "0.1-108",
  "Date": "2025-03-12",
  "Title": "Fast Algorithms for Generalized Principal Component Analysis",
  "Authors@R": "c(person(\"Eric\",\"Weine\",role=c(\"aut\",\"cre\"),\nemail=\"ericweine15@gmail.com\"),\nperson(\"Peter\",\"Carbonetto\",role=\"aut\"),\nperson(\"Matthew\",\"Stephens\",role=\"aut\"))",
  "Description": "Implements fast, scalable optimization algorithms for\nfitting generalized principal components analysis (GLM-PCA)\nmodels, as described in \"A Generalization of Principal\nComponents Analysis to the Exponential Family\" Collins M,\nDasgupta S, Schapire RE (2002, ISBN:9780262271738), and\nsubsequently \"Feature Selection and Dimension Reduction for\nSingle-Cell RNA-Seq Based on a Multinomial Model\" Townes FW,\nHicks SC, Aryee MJ, Irizarry RA (2019)\n<doi:10.1186/s13059-019-1861-6>.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/stephenslab/fastglmpca",
  "BugReports": "https://github.com/stephenslab/fastglmpca/issues",
  "SystemRequirements": "GNU make",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "make",
  "Repository": "https://stephenslab.r-universe.dev",
  "Date/Publication": "2025-03-12 12:34:52 UTC",
  "RemoteUrl": "https://github.com/stephenslab/fastglmpca",
  "RemoteRef": "HEAD",
  "RemoteSha": "4d7c3d145586ef562999c345a35174e03f54b35d",
  "Packaged": {
    "Date": "2026-07-09 08:34:17 UTC",
    "User": "root"
  },
  "Author": "Eric Weine [aut, cre],\nPeter Carbonetto [aut],\nMatthew Stephens [aut]",
  "Maintainer": "Eric Weine <ericweine15@gmail.com>",
  "_user": "stephenslab",
  "_type": "src",
  "_file": "fastglmpca_0.1-108.tar.gz",
  "_fileid": "https://r2.ropensci.org/69be9615517bcdb1486b3943147b66d48d95ca13cbae05674e000819498f1604",
  "_filesize": 3710724,
  "_sha256": "69be9615517bcdb1486b3943147b66d48d95ca13cbae05674e000819498f1604",
  "_expires": "2026-10-17T08:41:15.000Z",
  "_created": "2026-07-09T08:34:17.000Z",
  "_published": "2026-07-09T08:41:17.367Z",
  "_jobs": [
    {
      "job": 86075155458,
      "time": 217,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8193292918"
    },
    {
      "job": 86075155491,
      "time": 243,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8193302151"
    },
    {
      "job": 86075155550,
      "time": 212,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8193291204"
    },
    {
      "job": 86075155457,
      "time": 261,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8193308266"
    },
    {
      "job": 86075155523,
      "time": 129,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8193259923"
    },
    {
      "job": 86075155584,
      "time": 266,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8193310393"
    },
    {
      "job": 86075155497,
      "time": 214,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8193290649"
    },
    {
      "job": 86075155544,
      "time": 346,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8193340124"
    },
    {
      "job": 86074042175,
      "time": 351,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8193210214"
    },
    {
      "job": 86075155451,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8193272535"
    },
    {
      "job": 86075155447,
      "time": 216,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8193292424"
    },
    {
      "job": 86075155488,
      "time": 225,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8193294859"
    },
    {
      "job": 86075155473,
      "time": 209,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8193289845"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098",
  "_status": "success",
  "_upstream": "https://github.com/stephenslab/fastglmpca",
  "_commit": {
    "id": "4d7c3d145586ef562999c345a35174e03f54b35d",
    "author": "Eric Weine <ericw456@mit.edu>",
    "committer": "Eric Weine <ericw456@mit.edu>",
    "message": "update description\n",
    "time": 1741782892
  },
  "_maintainer": {
    "name": "Eric Weine",
    "email": "ericweine15@gmail.com",
    "login": "eweine",
    "description": "",
    "uuid": 71828618
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "RcppParallel",
      "role": "LinkingTo"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "distr",
      "role": "Imports"
    },
    {
      "package": "daarem",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.8",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.1.5",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    }
  ],
  "_owner": "stephenslab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 17,
  "_contributors": [
    {
      "user": "pcarbo",
      "count": 175,
      "uuid": 1503904
    },
    {
      "user": "eweine",
      "count": 160,
      "uuid": 71828618
    }
  ],
  "_userbio": {
    "uuid": 5939770,
    "type": "organization",
    "name": "Stephens lab",
    "followers": 118,
    "description": "Research in statistical and computational methods for genetics at the University of Chicago."
  },
  "_downloads": {
    "count": 348,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fastglmpca"
  },
  "_devurl": "https://github.com/stephenslab/fastglmpca",
  "_searchresults": 38,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fastglmpca.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/stephenslab/fastglmpca",
  "_realowner": "stephenslab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1-103",
      "date": "2024-01-31"
    },
    {
      "version": "0.1-107",
      "date": "2025-03-10"
    },
    {
      "version": "0.1-108",
      "date": "2025-03-13"
    }
  ],
  "_exports": [
    "fit_glmpca_pois",
    "fit_glmpca_pois_control_default",
    "generate_glmpca_data_pois",
    "init_glmpca_pois",
    "set_fastglmpca_threads"
  ],
  "_datasets": [
    {
      "name": "pbmc_facs",
      "title": "Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq data",
      "object": "pbmc_facs",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "fit_glmpca_pois",
      "title": "Fit Poisson GLM-PCA Model to Count Data",
      "topics": [
        "fit_glmpca_pois",
        "fit_glmpca_pois_control_default",
        "init_glmpca_pois"
      ]
    },
    {
      "page": "fitted.glmpca_pois_fit",
      "title": "Get Fitted Values for GLM-PCA Model Fit",
      "topics": [
        "fitted.glmpca_pois_fit"
      ]
    },
    {
      "page": "generate_glmpca_data_pois",
      "title": "Generate Data from a GLM-PCA Model",
      "topics": [
        "generate_glmpca_data_pois"
      ]
    },
    {
      "page": "pbmc_facs",
      "title": "Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq data",
      "topics": [
        "pbmc_facs"
      ]
    },
    {
      "page": "set_fastglmpca_threads",
      "title": "Set up Multithreading for fastglmpca",
      "topics": [
        "set_fastglmpca_threads"
      ]
    },
    {
      "page": "summary.glmpca_pois_fit",
      "title": "Summarize GLM-PCA Model Fit",
      "topics": [
        "print.summary.glmpca_pois_fit",
        "summary.glmpca_pois_fit"
      ]
    }
  ],
  "_readme": "https://github.com/stephenslab/fastglmpca/raw/HEAD/README.md",
  "_rundeps": [
    "daarem",
    "distr",
    "lattice",
    "MASS",
    "Matrix",
    "Rcpp",
    "RcppArmadillo",
    "RcppParallel",
    "sfsmisc",
    "startupmsg"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "intro_fastglmpca.Rmd",
      "filename": "intro_fastglmpca.html",
      "title": "Analysis of single-cell RNA-seq data using fastglmpca",
      "author": "Eric Weine and Peter Carbonetto",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The example data set",
        "Initializating and fitting the GLM-PCA model",
        "Session info"
      ],
      "created": "2023-11-09 21:50:21",
      "modified": "2024-01-23 15:14:47",
      "commits": 5
    }
  ],
  "_score": 5.509202522331103,
  "_indexed": true,
  "_nocasepkg": "fastglmpca",
  "_universes": [
    "stephenslab",
    "eweine"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:26.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/375bfbf71191bb82370673373bf9e45b8b4047e55586906c20c88079b8aa64a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/3512211e1702f512eb5e220910b7566f90fc171a8dbe3d6e491e9b5052708b7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:23.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/f9790afd2e0d6c0a5e087d222635e0468834e56e2f0b115d8094ed34db47db10",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:51.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/cdda747b4b1cc2a8a227e61665c498438f456dd3d4e1e9cc5b6d825c86b65e99",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1-108",
      "date": "2026-07-09T08:36:15.000Z",
      "arch": "aarch64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/494efe77729e8e414ae19e2ae0b62e5a4106177b4ca2c29f3818d4c201c2dae1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:23.000Z",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/6ef84dae83133962b46040ef6fe4228ca1b5a4cd8168c3777207a73d93373e1b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1-108",
      "date": "2026-07-09T08:36:33.000Z",
      "arch": "aarch64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/e3e511a2bfef976ec7d05d9719aaf2f380b5d181059e858ff8936a8dd08dd6cc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:47.000Z",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/ebec107357ff45a84be0250bd76710f594d3eda568c0a2926ec1db59ef270677",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1-108",
      "date": "2026-07-09T08:37:21.000Z",
      "arch": "emscripten",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/f1bd1a79d7b1a281fc8643f60903cf29f93dc9baef960e8eedd157fbe104c5cd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1-108",
      "date": "2026-07-09T08:36:21.000Z",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/140c478a9f0d3dfece92d490ae34c047f17b8bcaf646627db0fa391f41e3eab9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1-108",
      "date": "2026-07-09T08:36:08.000Z",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/7c2ecc3db923d54a06b71286a958b7d3eb7bb886dfe182fcc64b00d0cc471b3c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1-108",
      "date": "2026-07-09T08:36:07.000Z",
      "arch": "x86_64",
      "commit": "4d7c3d145586ef562999c345a35174e03f54b35d",
      "fileid": "https://r2.ropensci.org/26d718100b22e534e282b1439298f362c99e39cb03c399d39468c68cf6382d58",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29004812098"
    }
  ]
}