ImmuDef

Package: ImmuDef: A Novel Method for Quantitative Evaluation of Anti-infection Immune Defense Function and its Application

We created a python package called "ImmuDef" that uses RNA-seq data to compute quantitative assessments of an individual's immune defense function.

Requirements

Python Package Requirements

• Python 3.10
• scikit-learn 1.2.2
• numpy 1.23.5
• pandas 1.5.3

R Package Requirements

• R 4.3.2
• getopt 1.20.4
• tidyverse 2.0.0
• GSVA 1.50.1
• clusterProfiler 4.10.1
• msigdbr 7.5.1

Install Packages

• pip install git+https://github.com/GuoBioinfoLab/ImmuDef.git

Test

Run a test by python ./main.py

Transfer Learn to Your Own Dataset

• Prepare your dataset as a csv file which is ssGSEA data or RNA-seq data.

Start Compution

• Import this package. from immune_score.score_caculator import Immune_Score_Caculator
• Read your csv file as a pandas.DataFrame. data = pd.read_csv('Your_data', index_col=0).
• Compute immune scores. isc = Immune_Score_Caculator()
• Set data_type to 'Matrix' if your .csv files are RNA-seq data. immune_scores = isc.score_compute(data=data, data_type='Matrix', use_all_to_nor=True)
• Set data_type to 'ssGSEA' if your .csv files are already ssGSEA Data. immune_scores = isc.score_compute(data=data, data_type='Matrix', use_all_to_nor=True)

Cite

If you make use of the code/experiment in your work, please cite our paper (Bibtex below).

@article{ title={''}, author={''}, year={2024} }