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Bulk RNA-seq Deconvolution using Genetic Algorithm

A genetic algorithm implementation for deconvolving bulk RNA-seq data into cell type proportions.

Problem Description

Given:

  • M: Bulk expression matrix (genes x samples)
  • H: Reference signature matrix (genes x celltypes)

Find X (celltypes x samples) such that M = HX, where each column of X represents cell type proportions for a sample (summing to 1).

Installation

Prerequisites

  • Python >= 3.11
  • Poetry or pip

Using Poetry

poetry install
poetry run python main.py

Using pip

pip install numpy pandas matplotlib scipy
python main.py