Metadata-Version: 2.1
Name: cell2cell
Version: 0.5.0
Summary: TBD
Home-page: UNKNOWN
Author: cell2cell development team
Author-email: earmingol@eng.ucsd.edu
Maintainer: cell2cell development team
Maintainer-email: earmingol@eng.ucsd.edu
License: BSD-3-Clause
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Description-Content-Type: text/markdown
Requires-Dist: numpy (>=1.16)
Requires-Dist: pandas (>=1.0.0)
Requires-Dist: xlrd (>=1.1)
Requires-Dist: openpyxl (>=2.6.2)
Requires-Dist: networkx (>=2.3)
Requires-Dist: matplotlib (==3.1.2)
Requires-Dist: seaborn (==0.10.0)
Requires-Dist: scikit-learn
Requires-Dist: tqdm
Requires-Dist: statsmodels
Requires-Dist: tensorly
Requires-Dist: kneed
Requires-Dist: scanpy

# Inferring cell-cell interactions from transcriptomes with *cell2cell*
[![PyPI Version][pb]][pypi]
[![PyPI Downloads][db]][pypi]

[pb]: https://badge.fury.io/py/cell2cell.svg
[pypi]: https://pypi.org/project/cell2cell/
[db]: https://img.shields.io/pypi/dm/cell2cell?label=pypi%20downloads

## Installation
Create a new conda environment:
```
conda create -n cell2cell -y python=3.7 jupyter
```

Activate that environment:

```
conda activate cell2cell
```

Then, install cell2cell:
```
pip install cell2cell
```
## Examples

---
![plot](https://github.com/earmingol/cell2cell/blob/master/Logo.png?raw=true)
- A toy example using the **under-the-hood methods of cell2cell** is
  [available here](https://github.com/earmingol/cell2cell/blob/master/examples/cell2cell/Toy-Example.ipynb).
  This case allows personalizing the analyses in a higher level, but it may result **harder to use**.
- A toy example using an Interaction Pipeline for **bulk data** is 
  [available here](https://github.com/earmingol/cell2cell/blob/master/examples/cell2cell/Toy-Example-BulkPipeline.ipynb).
  An Interaction Pipeline makes cell2cell **easier to use**.
- A toy example using an Interaction Pipeline for **single-cell data** is 
  [available here](https://github.com/earmingol/cell2cell/blob/master/examples/cell2cell/Toy-Example-SingleCellPipeline.ipynb).
  An Interaction Pipeline makes cell2cell **easier to use**.  
- An example of using *cell2cell* to infer cell-cell interactions across the **whole
body of *C. elegans*** is [available here](https://github.com/LewisLabUCSD/Celegans-cell2cell)

---

![plot](https://github.com/earmingol/cell2cell/blob/master/LogoTensor.png?raw=true)
- A capsule containing jupyter notebooks for running Tensor-cell2cell (cell2cell v0.4.2) on datasets of **COVID-19 and the embryonic development
  of *C. elegans*** is [available in codeocean.com]()
- **Do you have precomputed communication scores?** Re-use them as a prebuilt tensor as [exemplified here](https://github.com/earmingol/cell2cell/blob/master/examples/tensor_cell2cell/Loading-PreBuiltTensor.ipynb).
  This allows reusing previous tensors you built or even plugging in communication scores from other tools.
- **Run Tensor-cell2cell much faster!** An example to perform the analysis using a **Nvidia GPU** is [available here](https://github.com/earmingol/cell2cell/blob/master/examples/tensor_cell2cell/GPU-Example.ipynb)


---

