A package to analyze celltypes on high definition spatial profiling assays

Installation

It is recommended to install the package in a virtual environment or a Conda environment. To create a Conda environment, run the following command:

conda create -n easydecon python=3.11
conda activate easydecon

You can install from PyPi:

pip install easydecon

To install directly from GitHub using pip into the active environment, run the following command:

pip install git+https://github.com/sinanugur/easydecon.git

Overview

Usage and Documentation

You may find our example notebooks in the notebooks folder.

• Demo notebook for a single-cell Anndata object (demo)[https://github.com/sinanugur/easydecon/blob/main/notebooks/demo.ipynb]
• Demo notebook for macrophage markers (demo_macrophage)[https://github.com/sinanugur/easydecon/blob/main/notebooks/demo_macrophage.ipynb]