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.flake8

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+[flake8]
+max-line-length = 88

.gitignore

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+*__pycache__*
+*.pyc
+results/*
+*.png
+*.jpg
+.snakemake
+
+.ipynb_checkpoints

README.md

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-# TrajectoryNet
+# Pytorch Implementation of TrajectoryNet
+
+This library runs code associated with the TrajectoryNet paper
+
+
+## Installation
+
+Download code
+```
+git clone http://github.com/krishanswamylab/TrajectoryNet.git
+```
+
+
+## Example
+<p align="center">
+<img align="middle" src="./figures/eb_high_quality.png" alt="EB PHATE Scatterplot" height="300" />
+<img align="middle" src="./figures/EB-Trajectory.gif" alt="Trajectory of density over time" height="300" />
+</p>
+
+## Basic Usage
+
+Run with
+```
+python main.py --dataset EB
+```
+
+To use a custom dataset expose the coordinates and timepoint information according to the `SCData` class in `dataset.py`
+
+### References
+[1] Tong, A., Huang, J., Wolf, G., van Dijk, D., and Krishnaswamy, S. TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. In International Conference on Machine Learning, 2020. [[arxiv]](http://arxiv.org/abs/2002.04461)
+
+---
+
+If you found this library useful, please consider citing
+```
+@inproceedings{tong2020trajectorynet,
+  title = {{{TrajectoryNet}}: {{A Dynamic Optimal Transport Network}} for {{Modeling Cellular Dynamics}}},
+  shorttitle = {{{TrajectoryNet}}},
+  booktitle = {Proceedings of the 37th {{International Conference}} on {{Machine Learning}}},
+  author = {Tong, Alexander and Huang, Jessie and Wolf, Guy and {van Dijk}, David and Krishnaswamy, Smita},
+  year = {2020}
+}
+```