Metadata-Version: 2.1
Name: ssam
Version: 1.1.1
Summary: SSAM
Home-page: https://github.com/pnucolab/ssam
Author: Jeongbin Park
Author-email: jeongbin.park@pusan.ac.kr
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
Classifier: Operating System :: POSIX
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: LICENSE.agpl
Requires-Dist: numpy <=2.0.2,>=1.26.4
Requires-Dist: zarr <3
Requires-Dist: networkx
Requires-Dist: numba
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: scikit-learn
Requires-Dist: umap-learn
Requires-Dist: leidenalg
Requires-Dist: sparse
Requires-Dist: scikit-image
Requires-Dist: dask
Requires-Dist: dask[array]
Requires-Dist: opencv-python
Requires-Dist: packaging
Requires-Dist: tqdm


SSAM (Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation)
========================================================================================

This repository contains the ongoing development of SSAM, including bugfixes, maintained by the Computational Omics Laboratory at Pusan National University (https://pnucolab.com).

If you are looking for the published version in 2021, please refer to https://github.com/HiDiHlabs/ssam.

Prerequisites
=============

Currently SSAM was only tested with Python 3 in Linux environment. For details, please follow the instructions here: https://ssam.readthedocs.io/en/release/tldr.html#installation

Install
=======

https://ssam.readthedocs.io/en/release/tldr.html#installation

Documentation
=============

https://ssam.readthedocs.io/

Citations
=========

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils & Naveed Ishaque. "`Cell segmentation-free inference of cell types from in situ transcriptomics data. <https://www.nature.com/articles/s41467-021-23807-4>`_" *Nature Communications* **12**, 3545 (2021). 

License
=======

Copyright (C) 2018 Jeongbin Park and Wonyl Choi

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published
by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see https://www.gnu.org/licenses/.
