{ "_id": "6ad1d6d929625c14e47aeb24", "Package": "SlimR", "Version": "1.2.0", "Title": "Adaptive Machine Learning Powered, Context Matching Tool for\nSingle-Cell and Spatial Transcriptomics Annotation", "Description": "Annotates single-cell and spatial-transcriptomic (ST) data\nusing context-matching marker datasets. It creates a unified\nmarker list (`Markers_list`) from multiple sources: built-in\ncurated databases ('Cellmarker2', 'PanglaoDB', 'ScType',\n'CellTypist', 'scBaseCount', 'scIBD', 'TCellSI', 'PCTIT',\n'PCTAM'), Seurat objects with cell labels, or user-provided\nExcel tables. SlimR first uses adaptive machine learning for\nparameter optimization, and then offers two automated\nannotation approaches: 'cluster-based' and 'per-cell'.\nCluster-based annotation assigns one label per cluster,\nexpression-based probability calculation, and AUC validation.\nPer-cell annotation assigns labels to individual cells using\nthree scoring methods with adaptive thresholds and ratio-based\nconfidence filtering, plus optional UMAP spatial smoothing,\nmaking it ideal for heterogeneous clusters and rare cell types.\nThe package also supports semi-automated workflows with\nheatmaps, feature plots, and combined visualizations for manual\nannotation. For more information, see the package documentation\nat .", "Authors@R": "person(given = \"Zhaoqing\",family = \"Wang\",\nemail = c(\"zhaoqingwang@mail.sdu.edu.cn\"),\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8348-7245\"))", "License": "MIT + file LICENSE", "URL": "https://github.com/zhaoqing-wang/SlimR", "BugReports": "https://github.com/zhaoqing-wang/SlimR/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "Date": "2026-10-16", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://zhaoqing-wang.r-universe.dev", "Date/Publication": "2026-10-16 03:10:50 UTC", "RemoteUrl": "https://github.com/zhaoqing-wang/slimr", "RemoteRef": "HEAD", "RemoteSha": "59dfb7f36d1cd6f3655830583fc7f6077159ff21", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 07:26:11 UTC", "User": "root" }, "Author": "Zhaoqing Wang 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