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Overview

SEnSCA, an innovative framework for unraveling the intricate network of cell-cell communication mediated by ligand-receptor interactions, integrates state-of-the-art machine learning algorithms and a three-point estimation methodology based on single-cell RNA sequencing data. SEnSCA accurately inferred intercellular communication within human melanoma tissues. It is anticipated to dissect cellular crosstalk and signal pathways at single cell resolution. Overview_SEnSCA

Environment

Install Python 3.9.16 for running this code. And these packages should be satisfied:

  • numpy=1.24.3
  • pandas=1.5.3
  • scikit-learn=1.2.2
  • torch=2.0.1
  • matplotlib=3.7.1

Data

  1. Ligand-receptor data is available at Uniprot, GEO.
  2. Feature extraction website at iFeature.

Usage

  • Step 1: Begin by running the code to identify reliable negative samples, with the option to manually adjust the pre value within the range of 0 to 1.
python Code/Kmeans.py
  • Step 2: Execute the code using the default 5-fold cross-validation, and get the ligand-receptor pairs.
python Code/SEnSCA.py
  • Step 3: Implement the three-point estimation method, incorporating [cell expression, expression product, specific expression]. (Note: the user-specified database only needs to replace the LRI.csv file and the corresponding format in the file.)
  • Step 4: Finally, output the strength of cell-cell communication.

Cell-cell communication tools for comparative analysis

CellChat iTALK CellPhoneDB NATMI CellComNet CellDialog Cellinker SingleCellSignalR Connectome Cytotalk

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