STCastl 0.1.1

A Consensus Framework for Robust Identification of Spatially Variable Genes in Spatial Transcriptomics

Castl: A Consensus Framework for Robust Identification of Spatially Variable Genes in Spatial Transcriptomics

1 Overview

Castl is a novel consensus-based analytical framework designed to enhance the accuracy and robustness of spatially variable genes identification for spatially resolved transcriptomics through statistically rigorous algorithms, including rank aggregation, p-value aggregation, and Stabl aggregation. Comprehensive evaluations on both simulated and real-world data demonstrate that Castl consistently identifies biologically meaningful spatial expression patterns, mitigates method-specific biases and effectively controls FDRs across various biological contexts, resolutions, and spatial technologies. This flexible, assumption-free framework offers a robust and standardized foundation for spatially informed feature discovery in complex biological systems.

2 System Requirements

Python

• Python >= 3.9.5
• pandas >= 1.3.0
• numpy >= 1.21.0
• rpy2 >= 3.5.0
• scipy >= 1.7.0
• statsmodels >= 0.13.0
• anndata >= 0.8.0
• scanpy >= 1.9.0
• matplotlib >= 3.5.0
• seaborn >= 0.12.0
• scikit-learn >= 1.0.0

R

• R >= 4.0.5
• dplyr >= 1.0.0
• tidyverse >= 1.3.0
• clusterProfiler >= 3.18.0
• org.Hs.eg.db >= 3.12.0
• patchwork >= 1.1.0
• ggplot2 >= 3.3.0
• TissueEnrich >= 1.8.0
• SummarizedExperiment >= 1.20.0

3 Installation

Python

Castl can be installed directly from PyPI：

pip install STCastl

or download from Github and install it:

git clone https://github.com/TheY11/Castl

cd Castl
pip install -e .

R

We also provide the R package castlRUtils for calculating quality scores (QS) of SVGs.

library(devtools)
devtools::install_github("TheY11/Castl", subdir = "Castl/r_utils", force = TRUE)
library(castlRUtils)

4 Tutorials

Detailed usage instructions and tutorials for Castl are available at: https://castl-analysis.readthedocs.io/en/latest/

5 Improvements

For questions or issues, please open an issue.