ComSeg 0.0.2

single cell RNA profiling analysis of imaging-based spatial transcriptomics data

ComSeg framework

A detail documentation is available Here https://comseg.readthedocs.io/en/latest/userguide.html

Single cell spatial RNA profiling

ComSeg is an algorithm for single cell spatial RNA profiling in image-based transcriptomic data.

It takes as input a csv with the spot coordinates and output an anndata object with the enes expression and coordinates of each cell.

Installation

First, create a dedicated conda environment using Python 3.8

conda create -n ComSeg python=3.8
conda activate ComSeg

To install the latest github version of this library run the following using pip

pip install git++https://github.com/tdefa/ComSeg

or alternatively you can clone the github repository

git clone +https://github.com/tdefa/ComSeg
cd cnn_framework
pip install -e .

A tutorial notebook can be found here : https://comseg.readthedocs.io/en/latest/userguide.html