Notice

This repository is no longer maintained. Further development of SSAM will be continued in the https://github.com/pnucolab/ssam repository.

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

Author: Jeongbin Park (jeongbin.park@charite.de)^1,2 and Wonyl Choi (wonyl@bu.edu)³

¹Digital Health Center, Berlin Institute of Health (BIH) and Charité – Universitätsmedizin, Berlin, Germany; ²Faculty of Biosciences, Heidelberg University, Heidelberg, Germany; ³Department of Computer Science, Boston University, Boston, the United States of America

(Not referring this 😆: https://en.wikipedia.org/wiki/Ssam)

This project was done under supervision of Dr. Naveed Ishaque (naveed.ishaque@charite.de) and Prof. Roland Eils (roland.eils@charite.de), and in collaboration with the SpaceTx consortium and the Human Cell Atlas project.

Please also check our example Jupyter notebooks here: https://github.com/eilslabs/ssam_example

Prerequisites

Currently SSAM was only tested with Python 3 in Linux environment. In addition to this package, SSAM requires a local R installation with pre-installed packages feather and sctransform. For details, please follow the instructions here: https://ssam.readthedocs.io/en/release/userguide/01-tldr.html#installation

Install

https://ssam.readthedocs.io/en/release/userguide/01-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." 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/.

License

HiDiHlabs/ssam

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