pilotpy 2.0.6
PILOT: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)
License: MIT
Requires Python: ==3.11.5

# PILOT 

[![GitHub license](https://img.shields.io/github/license/CostaLab/PILOT.svg)](https://github.com/CostaLab/PILOT?tab=MIT-1-ov-file#MIT-1-ov-file)

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

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

## [Tutorial&Data sets](https://pilot.readthedocs.io/en/latest/index.html)
There are five tutorials, one for [Myocardial Infarction (single cell data)](https://pilot.readthedocs.io/en/latest/Myocardial_infarction.html), and the second tutorial for [pathomics data, the combination of Kidney IgAN(G) & Kidney IgAN(T)](https://pilot.readthedocs.io/en/latest/Combination_Kidney_IgAN.html), and the third one  for [Patients sub-group detection and then ranking cells/genes (Pancreas data)](https://pilot.readthedocs.io/en/latest/Patients_sub_group_detection.html) and the forth one for 
[evaluation of the presence of batch effects in Trajectory](https://pilot.readthedocs.io/en/latest/Kidney_trajectory.html) and the last one for [evaluation of the presence of batch effects in detected sub-groups](https://pilot.readthedocs.io/en/latest/Kidney_clusters.html).


You can access the used data sets by PILOT in Part 1 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4740646.svg)](https://zenodo.org/records/8370081) and  Part 2 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4740646.svg)](https://zenodo.org/records/7957118)

# References
 PILOT: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT) [link](https://www.embopress.org/doi/full/10.1038/s44320-023-00003-8)