{
  "_id": "6ab0e53b3d719c1f840844e6",
  "Package": "SpaGER",
  "Type": "Package",
  "Title": "Spatial Gene Expression Prediction using scRNA-seq",
  "Version": "1.0.0",
  "Date": "2026-01-25",
  "Author": "Zaoqu Liu [aut, cre] (<https://orcid.org/0000-0002-0452-742X>),\nTamim Abdelaal [ctb] (Original SpaGE algorithm), Soufiane\nMourragui [ctb] (PRECISE algorithm)",
  "Maintainer": "Zaoqu Liu <liuzaoqu@163.com>",
  "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\")),\nperson(\"Tamim\", \"Abdelaal\", role = \"ctb\",\ncomment = \"Original SpaGE algorithm\"),\nperson(\"Soufiane\", \"Mourragui\", role = \"ctb\",\ncomment = \"PRECISE algorithm\")\n)",
  "Description": "Integrates spatial transcriptomics data with single-cell\nRNA sequencing (scRNA-seq) data to predict expression of\nunmeasured genes in spatial data. Uses Principal Vectors (PVs)\nfor domain adaptation followed by k-nearest neighbor weighted\nimputation. This R implementation provides identical results to\nthe original Python SpaGE package with efficient C++\nacceleration.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/Zaoqu-Liu/SpaGER",
  "BugReports": "https://github.com/Zaoqu-Liu/SpaGER/issues",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "yes",
  "SystemRequirements": "C++",
  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-24 17:55:59 UTC",
  "RemoteUrl": "https://github.com/Zaoqu-Liu/SpaGER",
  "RemoteRef": "main",
  "RemoteSha": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
  "Packaged": {
    "Date": "2026-09-21 07:58:17 UTC",
    "User": "root"
  },
  "_user": "zaoqu-liu",
  "_type": "src",
  "_file": "SpaGER_1.0.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/85d983f8fac4f429a0b1e70e6319376e6d1a60a39e5158cadcd8ef45a0b3ea04",
  "_filesize": 1097816,
  "_sha256": "85d983f8fac4f429a0b1e70e6319376e6d1a60a39e5158cadcd8ef45a0b3ea04",
  "_expires": "2026-12-30T08:05:13.000Z",
  "_created": "2026-09-21T07:58:17.000Z",
  "_published": "2026-09-21T08:05:15.234Z",
  "_jobs": [
    {
      "job": 106256404938,
      "time": 185,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10628271264"
    },
    {
      "job": 106256404953,
      "time": 174,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10627642726"
    },
    {
      "job": 106256404945,
      "time": 191,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10628326301"
    },
    {
      "job": 106256404990,
      "time": 202,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10627751333"
    },
    {
      "job": 106256404955,
      "time": 138,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10628500929"
    },
    {
      "job": 106256405060,
      "time": 367,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10628132010"
    },
    {
      "job": 106256405040,
      "time": 129,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10627676310"
    },
    {
      "job": 106256405184,
      "time": 361,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10628631014"
    },
    {
      "job": 106255247960,
      "time": 273,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10628260902"
    },
    {
      "job": 106256404880,
      "time": 168,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10628535927"
    },
    {
      "job": 106256405121,
      "time": 299,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10628216663"
    },
    {
      "job": 106256404973,
      "time": 185,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10628306312"
    },
    {
      "job": 106256405076,
      "time": 137,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10628480850"
    },
    {
      "job": 106256405035,
      "time": 247,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10627882059"
    },
    {
      "job": 106256405099,
      "time": 150,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10627599342"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788",
  "_status": "success",
  "_upstream": "https://github.com/Zaoqu-Liu/SpaGER",
  "_commit": {
    "id": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
    "author": "Zaoqu-Liu <liuzaoqu@163.com>",
    "committer": "Zaoqu-Liu <liuzaoqu@163.com>",
    "message": "build: Add pre-built vignettes to inst/doc\n\n- Build vignettes HTML and R files\n- Fix R CMD check vignette warnings\n- Update .Rbuildignore\n",
    "time": 1769277359
  },
  "_maintainer": {
    "name": "Zaoqu Liu",
    "email": "liuzaoqu@163.com",
    "login": "zaoqu-liu",
    "orcid": "0000-0002-0452-742X",
    "description": "AI4S",
    "uuid": 68080738
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "FNN",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "version": ">= 4.0.0",
      "role": "Suggests"
    },
    {
      "package": "SeuratObject",
      "role": "Suggests"
    },
    {
      "package": "fastICA",
      "role": "Suggests"
    },
    {
      "package": "NMF",
      "role": "Suggests"
    },
    {
      "package": "pls",
      "role": "Suggests"
    },
    {
      "package": "psych",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "zaoqu-liu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-04",
      "n": 8
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "zaoqu-liu",
      "count": 8,
      "uuid": 68080738
    }
  ],
  "_userbio": {
    "uuid": 68080738,
    "type": "user",
    "name": "LIU Zaoqu",
    "followers": 204,
    "description": "AI4S"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SpaGER"
  },
  "_devurl": "https://github.com/zaoqu-liu/spager",
  "_searchresults": 16,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SpaGER.html",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "check_seurat_version",
    "compare_expression",
    "compute_principal_vectors",
    "cosine_knn",
    "filter_genes",
    "knn_impute",
    "log_normalize",
    "log_normalize_median",
    "normalize_rows",
    "prepare_seurat",
    "process_dim_reduction",
    "PVComputation",
    "reset_parallel",
    "set_parallel",
    "SpaGE",
    "SpaGE_batch",
    "SpaGE_cv",
    "SpaGE.Seurat",
    "validate_input",
    "version_info",
    "zscore"
  ],
  "_help": [],
  "_readme": "https://github.com/Zaoqu-Liu/SpaGER/raw/main/README.md",
  "_rundeps": [
    "codetools",
    "digest",
    "FNN",
    "future",
    "future.apply",
    "globals",
    "irlba",
    "lattice",
    "listenv",
    "MASS",
    "Matrix",
    "parallelly",
    "Rcpp",
    "RcppArmadillo"
  ],
  "_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": "algorithm.Rmd",
      "filename": "algorithm.html",
      "title": "SpaGER: Algorithm and Mathematical Foundation",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "The Challenge",
        "Algorithm Steps",
        "Step 1: Data Standardization",
        "Step 2: Dimensionality Reduction",
        "Step 3: Matrix Orthogonalization",
        "Step 4: Principal Vectors Computation",
        "Step 5: Projection",
        "Step 6: Weighted k-NN Imputation",
        "Comparison with Python Implementation",
        "Summary",
        "References",
        "Session Information"
      ],
      "created": "2026-01-24 17:47:19",
      "modified": "2026-01-24 17:47:19",
      "commits": 1
    },
    {
      "source": "SpaGER_tutorial.Rmd",
      "filename": "SpaGER_tutorial.html",
      "title": "SpaGER: Quick Start Guide",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Why SpaGER?",
        "Installation",
        "Basic Usage",
        "Load Package",
        "Generate Simulated Data",
        "Run SpaGE Prediction",
        "Predict Specific Genes",
        "Cross-Validation",
        "Visualize CV Results",
        "Accessing Metadata",
        "Session Information"
      ],
      "created": "2026-01-24 17:12:11",
      "modified": "2026-01-24 17:47:19",
      "commits": 2
    },
    {
      "source": "seurat_integration.Rmd",
      "filename": "seurat_integration.html",
      "title": "SpaGER: Seurat Integration Guide",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Prerequisites",
        "Basic Workflow with Seurat",
        "Load Your Data",
        "Prepare Data (Optional)",
        "Run SpaGE",
        "Access Predictions",
        "Seurat v4 vs v5",
        "Explicit Version Control",
        "Predict Specific Genes",
        "Return Data Frame Instead",
        "Working with Different Assays",
        "Visualization After Prediction",
        "Batch Processing Multiple Gene Sets",
        "Tips for Best Results",
        "1. Matching Cell Types",
        "2. Gene Filtering",
        "3. Normalize Consistently",
        "Complete Example Workflow",
        "Troubleshooting",
        "Common Issues",
        "Session Information"
      ],
      "created": "2026-01-24 17:47:19",
      "modified": "2026-01-24 17:47:19",
      "commits": 1
    },
    {
      "source": "visualization.Rmd",
      "filename": "visualization.html",
      "title": "SpaGER: Visualization and Analysis",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Simulated Dataset",
        "Run SpaGE Prediction",
        "Visualizing Principal Vector Selection",
        "Spatial Expression Patterns",
        "Cross-Validation Results",
        "Measured vs Predicted Scatter Plots",
        "Expression Distribution Comparison",
        "Correlation Heatmap",
        "Summary Statistics",
        "Exporting Results",
        "Session Information"
      ],
      "created": "2026-01-24 17:47:19",
      "modified": "2026-01-24 17:47:19",
      "commits": 1
    }
  ],
  "_score": 3.5051499783199063,
  "_indexed": true,
  "_nocasepkg": "spager",
  "_universes": [
    "zaoqu-liu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:10.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/27aea3e3cfc9300e2982e464d23972da29b8fe767ab5766be7fc2c68c15a2ccb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:04.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/d3d83402797d404ae2657667e9c7b72573c9aee7324530c5af1dd9d0cfb495f1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:19.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/30b9722af1017b8c73afbd5eea1f9ed8e9e4bce87deeacea8404dd6fbc172ab6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:24.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/80d502c4bd71a740b2eced22cadde067f336e69cd223c75434613b1a917d7cd7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-09-21T08:00:21.000Z",
      "arch": "aarch64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/d8a787ac08bebba1aeadcbe69ba8942207f16390ede94887ecc6c336f0307488",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:50.000Z",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/167fb0ba1f21869eb4b8a14d6803ef0787942fa5c0b77693e9f3860fae7721d5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-09-21T08:00:11.000Z",
      "arch": "aarch64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/cb506418f97b96ebed25bdd724393e5b6470d508d38e3ccb1100688626f2763e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-09-21T08:02:45.000Z",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/f36be172c388816925306c332a301995830b941edc7b337a9005acde8897134a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:20.000Z",
      "arch": "emscripten",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/95e364f6f180f002e574fac0c185b32e4a1b1c8303eb3f20a032d2b14887c9d8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-09-21T08:02:46.000Z",
      "arch": "aarch64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/3651ca5b1fa54c5f45744889612b8f68b4046999bdd81a9fd92d57457b16bfe6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-09-21T07:59:57.000Z",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/a5fb337f11c6c6befa51d101d364ae1ff48ae5ee548a1e8d00660db154c26f2b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-09-21T08:00:01.000Z",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/523bfd48bd107dc8544d787ce4e9dd4febfe388871e091c7eb07e752d9f4da17",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-09-21T08:01:55.000Z",
      "arch": "aarch64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/34bdd43b40093c2a1c41ae25ab7152816ec08b2bc8df73c3a2ae660569caea65",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-09-21T08:00:00.000Z",
      "arch": "x86_64",
      "commit": "fa7fc0afbd10efeadfacc48984d5a253d375aff9",
      "fileid": "https://r2.ropensci.org/e6c5efd107b2a8ac85819d76f64ecd98c0dfe127d69e65e7a93bd700799df52d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/35575135788"
    }
  ]
}