SlimR: Marker-Based Package for Single-Cell and Spatial-Transcriptomic
Annotation
Annotating single-cell and spatial-transcriptomic (ST) data based on the Marker dataset. It supports the creation of a unified marker list, Markers_list, using sources including: the package's built-in curated species-specific cell type and marker reference databases (e.g., 'Cellmarker2', 'PanglaoDB'), Seurat objects containing cell label information, or user-provided Excel tables mapping cell types to markers.
Based on the Markers_list, 'SlimR' can iterate through different cell types to generate corresponding annotation reference plots (e.g., 'Markers_Dotplot', 'Metric_Heatmap', 'Mean_expression_Box_plot'). Furthermore, it enables one-click generation of an annotation heatmap ('Annotation_Heatmap') visualizing the relationship between input cell types and the reference marker list. For more details see Kabacoff (2015, ISBN:9781617291388) and Hu et al. (2023) <doi:10.1093/nar/gkac947> and Franzén et al. (2019) <doi:10.1093/database/baz046>.
| Version: |
1.0.3 |
| Depends: |
R (≥ 3.5) |
| Imports: |
cowplot, dplyr, ggplot2, patchwork, pheatmap, readxl, scales, Seurat, tidyr, tools, magrittr, tibble |
| Suggests: |
crayon |
| Published: |
2025-07-29 |
| DOI: |
10.32614/CRAN.package.SlimR |
| Author: |
Zhao qing Wang 
[aut, cre] |
| Maintainer: |
Zhao qing Wang <851091628 at qq.com> |
| License: |
GPL-3 |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
SlimR results |
Documentation:
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