Package: SlimR
Version: 1.2.0
Title: Adaptive Machine Learning Powered, Context Matching Tool for
        Single-Cell and Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data
        using context-matching marker datasets. It creates a unified
        marker list (`Markers_list`) from multiple sources: built-in
        curated databases ('Cellmarker2', 'PanglaoDB', 'ScType',
        'CellTypist', 'scBaseCount', 'scIBD', 'TCellSI', 'PCTIT',
        'PCTAM'), Seurat objects with cell labels, or user-provided
        Excel tables. SlimR first uses adaptive machine learning for
        parameter optimization, and then offers two automated
        annotation approaches: 'cluster-based' and 'per-cell'.
        Cluster-based annotation assigns one label per cluster,
        expression-based probability calculation, and AUC validation.
        Per-cell annotation assigns labels to individual cells using
        three scoring methods with adaptive thresholds and ratio-based
        confidence filtering, plus optional UMAP spatial smoothing,
        making it ideal for heterogeneous clusters and rare cell types.
        The package also supports semi-automated workflows with
        heatmaps, feature plots, and combined visualizations for manual
        annotation. For more information, see the package documentation
        at <https://github.com/zhaoqing-wang/SlimR>.
Authors@R: 
    person(given = "Zhaoqing",family = "Wang",
           email = c("zhaoqingwang@mail.sdu.edu.cn"),
           role = c("aut", "cre"),
           comment = 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
Depends: R (>= 4.1.0)
Imports: cowplot, dplyr, ggplot2, patchwork, pheatmap, readxl, scales,
        Seurat, tidyr, tools, tibble, gtools, RColorBrewer, methods
Suggests: crayon, RANN, testthat (>= 3.0.0), WeightedTreemaps
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
        libuv1-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: 2026-10-16 07:26:11 UTC; root
Author: Zhaoqing Wang [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8348-7245>)
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>