Single-Cell and Stereo-seq Spatial Transcriptomics Analysis Workflow

This project includes the complete workflow for single-cell and Stereo-seq spatial transcriptomics analysis, covering data quality control, integration analysis, spatial domain annotation, and main figure generation. The workflow is divided into three sections:

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1. Single-Cell Analysis

• Download specific cellxgene BICCN WHB single-cell data.
• Perform quality control on the raw single-cell data from this study.
• Integrate the processed single-cell data with BICCN datasets.

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2. Stereo-seq Analysis

• SquareBin Quality Control: Conduct basic quality control on Stereo-seq data.
• CellBin Quality Control: Further process the CellBin data.
• Spatial Domain Clustering and Annotation: Perform clustering and annotation of spatial domains based on SquareBin data.
• RCTD Deconvolution Annotation: Use single-cell data and RCTD to annotate spatial domains via deconvolution.

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3. Main Figure Generation

The figure generation scripts are organized according to the order of the manuscript's figures. Run the corresponding scripts after completing the single-cell and Stereo-seq analyses to generate the final results.

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Please follow the workflow in sequence to ensure data processing consistency. For any questions, contact the project lead.