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  1. Project Name: The name of your project.
  2. Description: A brief description of what your project does.
  3. Installation: Instructions for how to install your project.
  4. Usage: Instructions for how to use your project after it's installed.
  5. License: The license your project is distributed under.
  6. Note: This software package is yet to be published (unpublished)! If you have used it for publication purpose, please share authorship with MD. BABU MIA, PHD; ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI. Contact for detials: [email protected]

CellIdentifierDX

CellIdentifierDX is a Python package for identifying cell types using Bayesian scoring.

Installation

You can install CellIdentifierDX using pip:

pip install cellidentifierdx

Usage

Here's a basic example of how to use CellIdentifierDX:

from cellidentifierdx import annotate_cell_types

reference_file = "/path/to/your/reference_file.xlsx"
expr_file = "/path/to/your/expr_file.csv"
tissue, cell_type_annotations = annotate_cell_types(reference_file, expr_file, 'sheetname')

for cluster_idx, cell_type, avg_score in cell_type_annotations:
    print(f"Cluster {cluster_idx} is annotated as {cell_type} with average Bayesian score of {avg_score}.")

License

MIT