https://github.com/causalpathlab/spruceTopic

Single-cell Pairwise Relationships Untangled by Composite Topic models
https://github.com/causalpathlab/spruceTopic

Last synced: 4 months ago
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Single-cell Pairwise Relationships Untangled by Composite Topic models

• Host: GitHub
• URL: https://github.com/causalpathlab/spruceTopic
• Owner: causalpathlab
• License: mit
• Created: 2022-01-06T22:48:23.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-02-04T07:53:24.000Z (over 1 year ago)
• Last Synced: 2024-01-14T19:43:48.182Z (5 months ago)
• Language: Python
• Homepage:
• Size: 305 MB
• Stars: 0
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Lists

• awesome-cell-cell-communication - SPRUCE - [python]- SPRUCE is designed to systematically ascertain common cell-cell communication patterns embedded in single-cell RNA-seq data. (Uncategorized / Uncategorized)

README

        
## SPRUCE: Single-cell Pairwise Relationships Untangled by Composite Embedding model



    



###

This is a project repository for our paper-

* Subedi, S. and Park, Y.P.,  Single-cell Pairwise Relationships Untangled by Composite Embedding model,  iScience, 2023.

### Summary

In multi-cellular organisms, cell identity and functions are primed and refined through interactions with other surrounding cells. Here, we propose a scalable machine learning method, termed SPURCE, which is designed to systematically ascertain common cell-cell communication patterns embedded in single-cell RNA-seq data. We applied our approach to investigate tumour microenvironments consolidating multiple breast cancer data sets and found seven frequently-observed interaction signatures and underlying gene-gene interaction networks. Our results implicate that a part of tumour heterogeneity, especially within the same subtype, is better understood by differential interaction patterns rather than the static expression of known marker genes.

### Prerequisites

* python - numpy, pandas, scipy, sklearn, annoy, pytorch, igraph, seaborn

* R - celldex, SingleR, SingleCellExperiment, ggplot2, pheatmap, circlize, bipartite

### Dataset

 * Breast cancer cells 

 * Normal breast cells

 * Immune cells from breast Cancer 

### Installation

* Clone the repo

   ```sh

   git clone https://github.com/causalpathlab/spruceTopic.git

   ```