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CellWindX  

Marker Gene Analysis and Visualization for Single-Cell Data
View on CRAN: Click here


Download and install CellWindX package within the R console
Install from CRAN:
install.packages("CellWindX")

Install from Github:
library("remotes")
install_github("cran/CellWindX")

Install by package version:
library("remotes")
install_version("CellWindX", "1.0.0")



Attach the package and use:
library("CellWindX")
Maintained by
Xiaofeng Yang
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-05-27
Latest Update: 2026-05-27
Description:
Provides a 'Seurat'-compatible toolkit for marker gene identification, expression summarization, and visualization of annotated single-cell transcriptomic data. 'CellWindX' identifies top cell-type-enriched markers, calculates marker expression percentages and average expression values across cell groups, and generates publication-oriented dimensional reduction plots, marker heatmaps, and gene-level radar plots. The package includes built-in aesthetic palettes and supports both exploratory analysis and downstream figure preparation for single-cell atlas studies. The workflow is designed to complement single-cell analysis frameworks such as 'Seurat' described by Satija et al. (2015) <doi:10.1038/nbt.3192> and Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048>, as well as heatmap visualization methods implemented in 'ComplexHeatmap' described by Gu et al. (2016) <doi:10.1093/bioinformatics/btw313>.
How to cite:
Xiaofeng Yang (2026). CellWindX: Marker Gene Analysis and Visualization for Single-Cell Data. R package version 1.0.0, https://cran.r-project.org/web/packages/CellWindX. Accessed 26 Jun. 2026.
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Functions, R codes and Examples using the CellWindX R package
Full CellWindX package functions and examples
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