Metadata-Version: 2.1
Name: ComSeg
Version: 0.0.3
Summary: single cell RNA profiling analysis of imaging-based spatial transcriptomics data
Author-email: Thomas Defard <thomas.defard@mines-paristech.fr>
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata >=0.9.2
Requires-Dist: h5py >=3.9.0
Requires-Dist: networkx >=2.8.4
Requires-Dist: numba >=0.55.2
Requires-Dist: numpy >=1.22.4
Requires-Dist: pandas >=1.4.0
Requires-Dist: Pillow >=10.0.1
Requires-Dist: pyarrow >=13.0.0
Requires-Dist: rpds-py >=0.10.3
Requires-Dist: scanpy >=1.9.5
Requires-Dist: scikit-image >=0.21.0
Requires-Dist: scikit-learn >=1.0.1
Requires-Dist: scikit-misc >=0.2.0
Requires-Dist: scipy >=1.8.1
Requires-Dist: seaborn >=0.12.2
Requires-Dist: tifffile >=2023.7.10
Requires-Dist: tinycss2 >=1.2.1
Requires-Dist: tqdm >=4.66.1
Requires-Dist: traitlets >=5.11.2
Requires-Dist: umap-learn >=0.5.4
Requires-Dist: webencodings >=0.5.1
Requires-Dist: zipp >=3.16.2

# 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

```bash
conda create -n ComSeg python=3.8
conda activate ComSeg
```

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

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

or alternatively you can clone the github repository

```bash
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
