PILOT

Authors: Mehdi Joodaki^[1] ,Mina Shaigan^[1] ,Victor Parra^[1] ,Roman D. Bülow^[2] ,Christoph Kuppe^[3] ,David L. Hölscher^[2] ,Mingbo Cheng^[1] ,James S. Nagai^[1] ,Michaël Goedertier^[1,2] ,Nassim Bouteldja^[2] ,Vladimir Tesar^[5] ,Jonathan Barratt^[6,7] ,Ian S.D. Roberts^[8] ,Rosanna Coppo^[9] ,Rafael Kramann^[3,4] ,Peter Boorsup>[2,@]</sup ,Ivan G. Costasup>[1,@]</sup

Affiliations:

• [1] Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School
• [2] Institute of Pathology, Laboratory of Nephropathology, RWTH Aachen University Medical School
• [3] Institute of Experimental Medicine and Systems Biology, RWTH Aachen University
• [4] Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center
• [5] Department of Nephrology, $1^{st}$ Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
• [6] John Walls Renal Unit, University Hospital of Leicester National Health Service Trust, Leicester, United Kingdom
• [7] Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
• [8] Department of Cellular Pathology, Oxford University Hospitals National Health Services Foundation Trust, Oxford, United Kingdom
• [9] Fondazione Ricerca Molinette. Regina Margherita Children's University Hospital, Torino, Italy

Current version for PILOT is 2.0.6

Installation

The easiest way to install PILOT and the required packages is using the following way:

conda create --name PILOT python=3.11.5 r-base
conda activate PILOT
pip install pilotpy

Once you've completed these steps, you can proceed to run the tutorials and explore the features of PILOT. When doing so, remember to move to the tutorial folder, as all the work will be performed there:

git clone https://github.com/CostaLab/PILOT.git
cd PILOT/Tutorial

Tutorial&Data sets

There are five tutorials, one for Myocardial Infarction (single cell data), and the second tutorial for pathomics data, the combination of Kidney IgAN(G) & Kidney IgAN(T), and the third one for Patients sub-group detection and then ranking cells/genes (Pancreas data) and the forth one for evaluation of the presence of batch effects in Trajectory and the last one for evaluation of the presence of batch effects in detected sub-groups.

You can access the used data sets by PILOT in Part 1 and Part 2

Citation

@article{joodaki2024detection,
  title={Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)},
  author={Joodaki, Mehdi and Shaigan, Mina and Parra, Victor and B{\"u}low, Roman D and Kuppe, Christoph and H{\"o}lscher, David L and Cheng, Mingbo and Nagai, James S and Goedertier, Micha{\"e}l and Bouteldja, Nassim and others},
  journal={Molecular systems biology},
  volume={20},
  number={2},
  pages={57--74},
  year={2024},
  publisher={Nature Publishing Group UK London}
}