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https://github.com/plhhnu/CellGiQ
Cell-cell communication tool
https://github.com/plhhnu/CellGiQ
Last synced: 11 days ago
JSON representation
Cell-cell communication tool
- Host: GitHub
- URL: https://github.com/plhhnu/CellGiQ
- Owner: plhhnu
- Created: 2023-09-13T06:31:52.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-01-24T11:29:41.000Z (5 months ago)
- Last Synced: 2024-04-18T15:13:17.907Z (2 months ago)
- Language: Python
- Size: 41.4 MB
- Stars: 0
- Watchers: 0
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: readme.md
Lists
- awesome-cell-cell-communication - CellGiQ - [python]- CellGiQ is a a novel framework for deciphering ligand-receptor-mediated cell-cell communication by incorporating machine learning and a quartile scoring strategy. (Uncategorized / Uncategorized)
README
# CellGiQ
## Overview
CellGiQ, a novel framework for deciphering ligand-receptor-mediated cell-cell communication by incorporating machine learning and a quartile scoring strategy from single-cell RNA sequencing data. CellGiQ accurately inferred intercellular communication within human HNSCC tissues. CellGiQ is anticipated to dissect cellular crosstalk and signal pathways at
single cell resolution.
## Environment
- python == 3.8.13
### packages:
- tensorflow == 2.10.0
- keras == 2.10.0
- GBNN == 0.0.2
- interpret == 0.2.7
- scikit-learn == 0.24.0
- lightgbm == 3.3.5
- wheel == 0.37.1
- pands == 1.5.0
- numpy == 1.24.2
## Data
1.Data is available at [uniprot](https://www.uniprot.org/), [GEO](https://www.ncbi.nlm.nih.gov/geo/).
2.Feature extraction website at [BioTriangle](http://biotriangle.scbdd.com/)
## Usage
1. We obtain ligand and receptor feature at [BioTriangle](http://biotriangle.scbdd.com/)
2. Run the model to obtain the LRI, or the user-specified LRI database
```
python code/CellGiQ.py
```
3. Using quartile method (including Expression thresholding, Expression product and Specific expression), the cell-cell communication matrix was finally obtained.
```
python code/case study
```
## Change database
If you want to test other tumors, just replace `GSE103322.csv` in the code `case_study.py` (Note: use the specified database to replace the dataset`LRI_dataset.csv`)
## Cell-cell communication tools for comparative analysis
[CellChat](https://github.com/sqjin/CellChat) [iTALK](https://github.com/Coolgenome/iTALK) [LIANA](github.com/saezlab/liana) [CellPhoneDB](https://github.com/Teichlab/cellphonedb) [NATMI](https://github.com/asrhou/NATMI)