{
  "_id": "6ac9f1f7fe5cc25786e8321b",
  "Package": "RfmallocStatgen",
  "Title": "Statistical Genetics on Rfmalloc Genotype Tensors",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\", email = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Zilong\", family = \"Li\", role = \"cph\", comment = \"PCAone randomized-SVD core\")\n)",
  "Description": "Runs genome-scale statistical genetics methods over\nRfmalloc's file-backed, compressed genotype tensors ('bed' at 2\nbits per genotype, 'dosage' at 1 byte per genotype), closing\nover the analysis stack popularized by 'bigsnpr' and\n'bigstatsr' on denser storage with native readers, and adding\nhaplotype methods that a genotype-only stack cannot express.\nMethods are implemented from published algorithms and validated\nagainst 'bigsnpr' and 'bigstatsr' as numerical oracles. The\nexception is the randomized-SVD workhorse, which is pinned from\nGPL-3 'PCAone' (Li 2023) with a deterministic dependency trim\nand R-console adaptation. The current surface includes streamed\nunivariate regression and principal components, banded linkage\ndisequilibrium, LDpred2, and an all-pairs colocalisation\nexpressed as a single matrix multiply over any registered\ncompute backend.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Remotes": [
    "Rfmalloc=sounkou-bioinfo/Rfmalloc/packages/Rfmalloc",
    "Rggml=sounkou-bioinfo/Rfmalloc/packages/Rggml"
  ],
  "SystemRequirements": "C++17",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/sounkou-bioinfo/Rfmalloc,\nhttps://sounkou-bioinfo.github.io/Rfmalloc/RfmallocStatgen/",
  "BugReports": "https://github.com/sounkou-bioinfo/Rfmalloc/issues",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make",
  "Repository": "https://rgenomicsetl.r-universe.dev",
  "Date/Publication": "2026-09-09 23:54:20 UTC",
  "RemoteUrl": "https://github.com/RGenomicsETL/Rfmalloc",
  "RemoteRef": "HEAD",
  "RemoteSha": "156efa6ec133a512d8969fded81aaa630ff9ba16",
  "RemoteSubdir": "packages/RfmallocStatgen",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-10 07:46:39 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\nZilong Li [cph] (PCAone randomized-SVD core)",
  "Maintainer": "Sounkou Mahamane Toure <sounkoutoure@gmail.com>",
  "_user": "rgenomicsetl",
  "_type": "src",
  "_file": "RfmallocStatgen_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/ef6ab81bae2f2a06dc9b304879748d0954af950772552c2ae3d3761db9085f9b",
  "_filesize": 255712,
  "_sha256": "ef6ab81bae2f2a06dc9b304879748d0954af950772552c2ae3d3761db9085f9b",
  "_expires": "2027-01-18T08:06:13.000Z",
  "_created": "2026-10-10T07:46:39.000Z",
  "_published": "2026-10-10T08:06:14.946Z",
  "_buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114165342088,
      "time": 175,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11663374202"
    },
    {
      "job": 114165342140,
      "time": 170,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11663516934"
    },
    {
      "job": 114165342210,
      "time": 119,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11663916723"
    },
    {
      "job": 114165342093,
      "time": 162,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11663411952"
    },
    {
      "job": 114165342148,
      "time": 126,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11664557661"
    },
    {
      "job": 114165342158,
      "time": 281,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11664153265"
    },
    {
      "job": 114165342155,
      "time": 132,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11664303039"
    },
    {
      "job": 114165342099,
      "time": 264,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11664378021"
    },
    {
      "job": 114164600284,
      "time": 263,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11663751535"
    },
    {
      "job": 114165342083,
      "time": 125,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11663696025"
    },
    {
      "job": 114165342127,
      "time": 234,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11664336662"
    },
    {
      "job": 114165342153,
      "time": 178,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11663427161"
    },
    {
      "job": 114165342131,
      "time": 162,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11663920932"
    },
    {
      "job": 114165342167,
      "time": 208,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11663961091"
    },
    {
      "job": 114165342157,
      "time": 156,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11663427130"
    }
  ],
  "_upstream": "https://github.com/RGenomicsETL/Rfmalloc",
  "_commit": {
    "id": "156efa6ec133a512d8969fded81aaa630ff9ba16",
    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "committer": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "message": "Keep the shared library the default goal in the statgen Makevars\n",
    "time": 1788998060
  },
  "_maintainer": {
    "name": "Sounkou Mahamane Toure",
    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
    "uuid": 56392505
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "Rfmalloc",
      "role": "Depends"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "Rfmalloc",
      "role": "LinkingTo"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Rggml",
      "role": "Suggests"
    },
    {
      "package": "Rpgen",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    },
    {
      "package": "bigsnpr",
      "role": "Suggests"
    },
    {
      "package": "bigstatsr",
      "role": "Suggests"
    },
    {
      "package": "bigsparser",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "pcaone",
      "role": "Suggests"
    }
  ],
  "_owner": "rgenomicsetl",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-19",
      "n": 50
    },
    {
      "week": "2026-20",
      "n": 6
    },
    {
      "week": "2026-23",
      "n": 1
    },
    {
      "week": "2026-28",
      "n": 83
    },
    {
      "week": "2026-29",
      "n": 16
    },
    {
      "week": "2026-31",
      "n": 1
    },
    {
      "week": "2026-37",
      "n": 10
    }
  ],
  "_tags": [],
  "_topics": [
    "altrep",
    "blas",
    "genomics",
    "ggml",
    "gguf",
    "llm",
    "llm-inference",
    "malloc",
    "memory-mapped",
    "mmap",
    "out-of-core",
    "quantization",
    "simd",
    "cpp"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "sounkou-bioinfo",
      "count": 218,
      "uuid": 56392505
    }
  ],
  "_userbio": {
    "uuid": 252609706,
    "type": "organization",
    "name": "GenomicsETL",
    "followers": 10,
    "description": "Composable genomics in DuckDB, with R, the browser and agents as front ends"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RfmallocStatgen"
  },
  "_devurl": "https://github.com/sounkou-bioinfo/rfmalloc",
  "_searchresults": 6,
  "_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/RfmallocStatgen.html"
  ],
  "_cranurl": false,
  "_exports": [
    "statgen_coloc_bf",
    "statgen_gwas_lin",
    "statgen_ldpred2",
    "statgen_ldpred2_auto",
    "statgen_ldpred2_inf",
    "statgen_pca",
    "statgen_snp_cor"
  ],
  "_help": [
    {
      "page": "statgen_coloc_bf",
      "title": "Colocalisation of two traits' signals by Bayes factors (all pairs at once)",
      "topics": [
        "statgen_coloc_bf"
      ]
    },
    {
      "page": "statgen_gwas_lin",
      "title": "Univariate linear-regression GWAS over an fmalloc genotype tensor",
      "topics": [
        "statgen_gwas_lin"
      ]
    },
    {
      "page": "statgen_ldpred2",
      "title": "LDpred2: Bayesian polygenic scores over a banded LD matrix",
      "topics": [
        "statgen_ldpred2",
        "statgen_ldpred2_auto",
        "statgen_ldpred2_inf"
      ]
    },
    {
      "page": "statgen_pca",
      "title": "Fast principal-component analysis by PCAone randomized SVD",
      "topics": [
        "statgen_pca"
      ]
    },
    {
      "page": "statgen_snp_cor",
      "title": "Windowed LD (correlation) matrix from a genotype tensor",
      "topics": [
        "statgen_snp_cor"
      ]
    }
  ],
  "_readme": "https://github.com/RGenomicsETL/Rfmalloc/raw/HEAD/packages/RfmallocStatgen/README.md",
  "_rundeps": [
    "Rcpp",
    "RcppEigen",
    "Rfmalloc"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.146128035678238,
  "_indexed": true,
  "_nocasepkg": "rfmallocstatgen",
  "_universes": [
    "rgenomicsetl",
    "sounkou-bioinfo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-10T07:49:46.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/dbc0147fa481cb5778852ba1f9adf96a648177e38782c5e599982bdc51729688",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-10T07:49:26.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/9a84537ff02b4f5b8eef81930e9ea6e320a102333e5521fad3fde25d21afcc38",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-10T07:48:56.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/44aafdac2f47de245651a76e17911e75146736c9abb898260fabe0497a93d1d2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-10T07:49:21.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/536811b7b806eb7db18bd8ae801b703e2e22ee65108d832ca121e5c451e46eb6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-10T08:03:52.000Z",
      "arch": "aarch64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/a8e0750a8198ee694ecc8fef30304d2f98f0d66640a2df888ad4078668c3adaa",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-10T08:04:06.000Z",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/37e30c976fe43b6688ed1036b6588ee74e65c9540265bbb7b823bb81c651b6d0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-10T08:04:55.000Z",
      "arch": "aarch64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/e1b8de97e98633c4a7121a02937fb0aadb3929c8028791bda3c7c4abf4f5eb3d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-10T08:03:07.000Z",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/92b062f3f0d4cab643379e44f61ee61b86255a39867305a220429d41bbfc604e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-10-10T07:49:10.000Z",
      "arch": "emscripten",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/764827ca448b0486e0347bd1c6a8909944a7b61ba621838506c2de5b87f17b61",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-10T07:50:26.000Z",
      "arch": "aarch64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/150cf42c89484141a28bd31ac86d8b6cd7b93645d8234c3678f558daa9ee49b3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-10T07:48:30.000Z",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/b94f7c20e96d76dff59b6d42a9bbdb52bb1171385b09d78cccc701ed1b62cbf6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-10T07:48:33.000Z",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/0715488f7ac0103f1a9f27aa84f13b8139bb0d518adf76600cf3ef52b0f5040a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-10T07:50:05.000Z",
      "arch": "aarch64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/37709e7f4b5cf7f4f460f11621f2155ee81cad7553f33403314b1cb9fbf015c8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-10T07:48:42.000Z",
      "arch": "x86_64",
      "commit": "156efa6ec133a512d8969fded81aaa630ff9ba16",
      "fileid": "https://r2.ropensci.org/786911b08e0085bbfe95a47582d6508c56c211df1eedf151f40818ee0b3c2386",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38035360896"
    }
  ]
}