Package: SlimR
Version: 1.1.6
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',
        '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
Suggests: crayon, RANN, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
Date: 2026-06-30
Config/roxygen2/version: 8.0.0
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: 2026-07-01 16:19:14 UTC
RemoteUrl: https://github.com/zhaoqing-wang/slimr
RemoteRef: HEAD
RemoteSha: d84f47d462b1e0cb65978df2791f4b0d9eee7c89
NeedsCompilation: no
Packaged: 2026-07-01 17:58:02 UTC; root
Author: Zhaoqing Wang [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8348-7245>)
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>