README.md

ImmuCellAI 2.0

ImmuCellAI 2.0 is an advanced bulk transcriptome deconvolution tool for immunogenomic research, optimized to accurately infer the relative proportions of immune cell populations from bulk RNA-seq data. It supports the quantification of 9 major immune cell types and 53 minor functional subtypes (including rare subsets like exhausted B/T cells, tissue-resident memory T cells, and tumor-associated macrophages).

Quick Access

• Web Server (no programming required): https://guolab.wchscu.cn/ImmuCellAI2/
• GitHub Repository: https://github.com/GuoBioinfoLab/ImmuCellAI-2.0/

ImmuCellAI 2.0 Python Package

Prerequisites

• Python 3.8+

Install using pip

pip install immucellai2

Usage

ImmuCellAI 2.0 expects a TPM matrix as input and can be implemented with only two lines of code in Python.

import immucellai2
reference_data = immucellai2.load_tumor_reference_data()

result = immucellai2.run_ImmuCellAI2(
    reference_file=reference_data,
    sample_file=<file_path>,    #  User-defined
    output_file=<file_path>,    #  User-defined
    thread_num=8
)

Citation