BrainRep

This script codes for a predictive algorithm that uses gene expression data of human brain cells and regulatory network information to predict transcription factors for inducing cell reprogramming between specific brain cells and neuronal subtypes.

Files

• brain_cells_data.json : file containing the identifiers of the brain cells and neuronal subtypes that can be used as source cell or desired cell --types, and the brain region where they are present
  
• brain_rep.py : main script
  
• br_utils.py : script containing helper functions
  
• brain_qc.h5ad : raw gene expression file (NOT uploaded to GitHub)
  
• trimmed_means.csv : log-transformed gene expression file (NOT uploaded to GitHub)
  

Usage

brain_rep.py [-h] -s SOURCECELL -d DESIREDCELL [-o ORGANISM]

Example

python3 brain_rep.py -s "Neuron 001" -d "Neuron 051"