eveilyeverafter / cosmx-analysis-scratch-space

CosMx Analysis Scratch Space

This repo is here to accelerate analysis of CosMx datasets. It contains code and writeups addressing challenges we've faced in analyzing CosMx data. After dozens of analyses, we have developed a sense of what works and what doesn't, and we have developed (sometimes partial) solutions for many frequent problems.

Code in this repo is provided without warranty or promise of support. This is not official NanoSting software and has not been subjected to the usual rigorous review and testing.

For questions or suggestions, write an Issue. Contributions are welcome from the community - just reach out to get write permission.

Table of contents

• Items with a checkbox like this are awaiting material.

Data formats

• File structure output by the AtoMx export module
• Converting between data formats: AtoMx flat files, Seurat, squidpy

Analysis strategies

• What is spatial data for?
• QC and normalization of RNA data
• Batch correction
• The spatial algorithms zoo: recommended algorithms and efficient code
• A generally satisfying set of UMAP parameters for CosMx data
• The impact of segmentation error on differential expression analyses
• Quick & comprehensive searches for interesting trends with "Everything vs. everything DE"
• Smoothing single cell gene expression for enhanced plotting
• Approaches to ligand-receptor analysis
• Big datasets: strategies for memory-efficient analysis
• lots without excessive file sizes
• Functions for condensing FOVs and tissues to minimize whitespace
• Inferring cell polygons from transcript locations
• (For fun) Spatial transcriptomics plots in stained glass
• Visualization of cellular neighborhood in gallery mode

Cell typing

• Cell typing: what we've found to work
• On the use of marker genes
• Hierarchical ("plinko") cell typing
• Cell typing with smoothed marker genes
• Integrating spatial information and/or cell images into existing cell typing results

Tissue-specific solutions

• A workflow for kidney samples: cell typing and glomerulus definitions
• Scoring brain cells for distance to plaques

License

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