{ "_id": "6a215e92cd65a98ecbd2fd5d", "Package": "SlimR", "Version": "1.1.5", "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'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects with cell\nlabels, or user-provided Excel tables. SlimR first uses\nadaptive machine learning for parameter optimization, and then\noffers two automated annotation approaches: 'cluster-based' and\n'per-cell'. Cluster-based annotation assigns one label per\ncluster, expression-based probability calculation, and AUC\nvalidation. Per-cell annotation assigns labels to individual\ncells using three scoring methods with adaptive thresholds and\nratio-based confidence filtering, plus optional UMAP spatial\nsmoothing, making it ideal for heterogeneous clusters and rare\ncell types. The package also supports semi-automated workflows\nwith heatmaps, feature plots, and combined visualizations for\nmanual annotation. For more information, see the package\ndocumentation at .", "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": "2026-06-03", "Config/roxygen2/version": "8.0.0", "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": "2026-06-04 09:46:37 UTC", "RemoteUrl": "https://github.com/zhaoqing-wang/slimr", "RemoteRef": "HEAD", "RemoteSha": "b7d9013c4200291ca8470676416aca18a84fff7b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 11:06:07 UTC", "User": "root" }, "Author": "Zhaoqing Wang 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