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:

Reference manual:

SlimR.html , SlimR.pdf

Downloads:

Package source:	SlimR_1.0.3.tar.gz
Windows binaries:	r-devel: SlimR_1.0.3.zip, r-release: SlimR_1.0.3.zip, r-oldrel: SlimR_1.0.3.zip
macOS binaries:	r-release (arm64): SlimR_1.0.3.tgz, r-oldrel (arm64): SlimR_1.0.3.tgz, r-release (x86_64): SlimR_1.0.3.tgz, r-oldrel (x86_64): SlimR_1.0.3.tgz

Linking:

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