{
  "_id": "6a1ee78db401979e734117e5",
  "Package": "leo.sc",
  "Title": "Layered Exploratory Omics (LEO for single-cell analysis)",
  "Version": "0.1.0",
  "Authors@R": "person(\"Ao\", \"Lu\", , \"luao@stu.cqmu.edu.cn\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0001-0927-4468\"))",
  "Description": "LEO for single-cell analysis. This package provides useful\nfunctions for single-cell analysis workflow.",
  "License": "GPL (>= 3)",
  "URL": "https://laleoarrow.github.io/leo.sc/,\nhttps://github.com/laleoarrow/leo.sc",
  "BugReports": "https://github.com/laleoarrow/leo.sc/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Remotes": [
    "laleoarrow/leo.basic",
    "chris-mcginnis-ucsf/DoubletFinder",
    "PaulingLiu/ROGUE",
    "neurorestore/Augur",
    "powellgenomicslab/Nebulosa"
  ],
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev perl python3\nzlib1g-dev",
  "Repository": "https://laleoarrow.r-universe.dev",
  "Date/Publication": "2026-03-04 05:03:03 UTC",
  "RemoteUrl": "https://github.com/laleoarrow/leo.sc",
  "RemoteRef": "HEAD",
  "RemoteSha": "3e2d81c5590e42fe17d72d4fbb19a4bf46b71a13",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-19 17:17:40 UTC",
    "User": "root"
  },
  "Author": "Ao Lu [aut, cre] (ORCID: <https://orcid.org/0009-0001-0927-4468>)",
  "Maintainer": "Ao Lu <luao@stu.cqmu.edu.cn>",
  "MD5sum": "e6f602d6b1c5ad79af6253e453def883",
  "_user": "laleoarrow",
  "_type": "src",
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  "_created": "2026-05-19T17:17:40.000Z",
  "_published": "2026-06-02T14:24:13.432Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/laleoarrow/actions/runs/26112948453",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/laleoarrow/leo.sc",
  "_commit": {
    "id": "3e2d81c5590e42fe17d72d4fbb19a4bf46b71a13",
    "author": "Ao Lu <luao@stu.cqmu.edu.cn>",
    "committer": "Ao Lu <luao@stu.cqmu.edu.cn>",
    "message": "fix: resolve R CMD check WARNING and NOTE\n\n- metadata.R: replace Seurat::subset() with subset() — Seurat::subset\n  is an S3 method and is not exported from the Seurat namespace, causing\n  'Missing or unexported object' WARNING\n- basic.R (metadata_write_10x): replace bare dplyr::select(barcode, ...)\n  with dplyr::select(all_of(c('barcode', keep_cols))) to eliminate\n  'no visible binding for global variable barcode' NOTE\n",
    "time": 1772600583
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  "_maintainer": {
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    "email": "luao@stu.cqmu.edu.cn",
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  "_owner": "laleoarrow",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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  "_tags": [
    {
      "name": "LEO",
      "date": "2025-08-06"
    },
    {
      "name": "data-v2",
      "date": "2026-03-03"
    }
  ],
  "_topics": [
    "genetics",
    "single-cell"
  ],
  "_stars": 1,
  "_contributors": [
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      "uuid": 127536391
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  "_userbio": {
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/leo.sc"
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  "_assets": [
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    "extra/citation.json",
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    "extra/readme.html",
    "extra/readme.md",
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  "_cranurl": false,
  "_exports": [
    "calcROGUE",
    "check_gene_avg_in_multi_batch",
    "check_gene_stats_in_multi_batch",
    "doublet_rate_dictionary",
    "doublet_removal",
    "filter_clusters_by_percent_or_cell_count",
    "format_markers_for_upload",
    "get_cluster_counts",
    "gimme_marker",
    "leo_milo_vis",
    "leo.augur",
    "leo.marker",
    "leo.milo",
    "leo.ROIE",
    "locate_most_different_g_in_2_group",
    "metadata_drop",
    "metadata_get_colnames",
    "metadata_keep",
    "metadata_write_10x",
    "plot_alluvial",
    "plot_alluvial_sc",
    "plot_dbee",
    "plot_gw_density",
    "plot_highlight_cluster",
    "plot_qc",
    "plot_score_signature_heatmap",
    "read_sc_data",
    "remove_unwant_hvg",
    "ROIE",
    "score_signature",
    "seurat_basic_info",
    "seurat_basic_qc",
    "seurat_standard_normalize_and_scale",
    "silico_ko",
    "sort_string_numeric_clusters",
    "subset_common_gene_in_multi_batch",
    "subset_srt",
    "write_10x_triple"
  ],
  "_help": [
    {
      "page": "calcROGUE",
      "title": "Calculate and plot ROGUE index for a Seurat object, with inline filtering",
      "topics": [
        "calcROGUE"
      ]
    },
    {
      "page": "check_gene_stats_in_multi_batch",
      "title": "Inspection of gene in multi-batch",
      "topics": [
        "check_gene_avg_in_multi_batch",
        "check_gene_stats_in_multi_batch",
        "subset_common_gene_in_multi_batch"
      ]
    },
    {
      "page": "doublet_rate_dictionary",
      "title": "Lookup expected doublet rate based on cells loaded",
      "topics": [
        "doublet_rate_dictionary"
      ]
    },
    {
      "page": "doublet_removal",
      "title": "Remove doublets using DoubletFinder",
      "topics": [
        "doublet_removal"
      ]
    },
    {
      "page": "filter_clusters_by_percent_or_cell_count",
      "title": "Filter Seurat clusters by percentage or absolute cell count",
      "topics": [
        "filter_clusters_by_percent_or_cell_count"
      ]
    },
    {
      "page": "format_markers_for_upload",
      "title": "Format marker-gene lists for (bulk) upload",
      "topics": [
        "format_markers_for_upload"
      ]
    },
    {
      "page": "get_cluster_counts",
      "title": "Get cluster counts sorted descending",
      "topics": [
        "get_cluster_counts"
      ]
    },
    {
      "page": "gimme_marker",
      "title": "Give me marker!",
      "topics": [
        "gimme_marker"
      ]
    },
    {
      "page": "leo_milo_vis",
      "title": "Visualize MiloR DA results",
      "topics": [
        "leo_milo_vis"
      ]
    },
    {
      "page": "leo.augur",
      "title": "Run Augur analysis",
      "topics": [
        "leo.augur"
      ]
    },
    {
      "page": "leo.marker",
      "title": "Marker hub",
      "topics": [
        "leo.marker"
      ]
    },
    {
      "page": "leo.milo",
      "title": "Run Milo differential abundance workflow on a Seurat object",
      "topics": [
        "leo.milo"
      ]
    },
    {
      "page": "leo.ROIE",
      "title": "Compute Ro/e and draw heatmap",
      "topics": [
        "leo.ROIE"
      ]
    },
    {
      "page": "locate_most_different_g_in_2_group",
      "title": "Locate most distinguishing markers between two clusters",
      "topics": [
        "locate_most_different_g_in_2_group"
      ]
    },
    {
      "page": "metadata_drop",
      "title": "Drop specified metadata columns from a Seurat object",
      "topics": [
        "metadata_drop"
      ]
    },
    {
      "page": "metadata_get_colnames",
      "title": "Get specified metadata columns from a Seurat object",
      "topics": [
        "metadata_get_colnames"
      ]
    },
    {
      "page": "metadata_keep",
      "title": "Keep only selected metadata columns in a Seurat object",
      "topics": [
        "metadata_keep"
      ]
    },
    {
      "page": "metadata_write_10x",
      "title": "Export Seurat meta.data aligned to barcodes",
      "topics": [
        "metadata_write_10x"
      ]
    },
    {
      "page": "plot_alluvial",
      "title": "Draw alluvial bars with optional custom palette",
      "topics": [
        "plot_alluvial"
      ]
    },
    {
      "page": "plot_alluvial_sc",
      "title": "Alluvial plot from a Seurat object",
      "topics": [
        "plot_alluvial_sc"
      ]
    },
    {
      "page": "plot_dbee",
      "title": "Different-effect-variable Beeswarm Plot",
      "topics": [
        "plot_dbee"
      ]
    },
    {
      "page": "plot_gw_density",
      "title": "Plot gene-weighted density",
      "topics": [
        "plot_gw_density"
      ]
    },
    {
      "page": "plot_highlight_cluster",
      "title": "Highlight a cluster",
      "topics": [
        "plot_highlight_cluster"
      ]
    },
    {
      "page": "plot_qc",
      "title": "Plot QC metrics",
      "topics": [
        "plot_qc"
      ]
    },
    {
      "page": "plot_score_signature_heatmap",
      "title": "Plot heatmap of signature scores",
      "topics": [
        "plot_score_signature_heatmap"
      ]
    },
    {
      "page": "read_sc_data",
      "title": "Read single-cell data into a Seurat object",
      "topics": [
        "read_sc_data"
      ]
    },
    {
      "page": "remove_unwant_hvg",
      "title": "Remove unwanted HVGs",
      "topics": [
        "remove_unwant_hvg"
      ]
    },
    {
      "page": "ROIE",
      "title": "Calculate ROIE",
      "topics": [
        "ROIE"
      ]
    },
    {
      "page": "score_signature",
      "title": "Score sc_obj with signature list",
      "topics": [
        "score_signature"
      ]
    },
    {
      "page": "seurat_basic_info",
      "title": "get basic summary of a seurat object",
      "topics": [
        "seurat_basic_info"
      ]
    },
    {
      "page": "seurat_basic_qc",
      "title": "Seurat basic QC",
      "topics": [
        "seurat_basic_qc"
      ]
    },
    {
      "page": "seurat_standard_normalize_and_scale",
      "title": "Standard seurat normalize_and_scale",
      "topics": [
        "seurat_standard_normalize_and_scale"
      ]
    },
    {
      "page": "silico_ko",
      "title": "In-silico Knock-Out / Knock-In Analysis (single gene)",
      "topics": [
        "silico_ko"
      ]
    },
    {
      "page": "sort_string_numeric_clusters",
      "title": "Sort string-based cluster labels numerically and refactor",
      "topics": [
        "sort_string_numeric_clusters"
      ]
    },
    {
      "page": "subset_srt",
      "title": "Subset srt obj easily",
      "topics": [
        "subset_srt"
      ]
    },
    {
      "page": "write_10x_triple",
      "title": "Export Seurat object to 10x-style triple files",
      "topics": [
        "write_10x_triple"
      ]
    }
  ],
  "_readme": "https://github.com/laleoarrow/leo.sc/raw/HEAD/README.md",
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