https://github.com/cbg-ethz/scatrex

Map single-cell transcriptomes to copy number evolutionary trees.
https://github.com/cbg-ethz/scatrex

cancer-genomics copy-number-variation jax scrna-seq

Last synced: about 2 months ago
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Map single-cell transcriptomes to copy number evolutionary trees.

• Host: GitHub
• URL: https://github.com/cbg-ethz/scatrex
• Owner: cbg-ethz
• License: other
• Created: 2021-11-03T16:13:52.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2022-11-21T15:58:06.000Z (about 2 years ago)
• Last Synced: 2024-03-26T08:10:22.853Z (9 months ago)
• Topics: cancer-genomics, copy-number-variation, jax, scrna-seq
• Language: Python
• Homepage: https://www.biorxiv.org/content/10.1101/2021.11.04.467244v1
• Size: 3.79 MB
• Stars: 13
• Watchers: 3
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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Map single-cell transcriptomes to copy number evolutionary trees. Check out the [tutorial](https://github.com/cbg-ethz/SCATrEx/blob/main/notebooks/tutorial.ipynb) for more information.

## Installation

```

$ pip install scatrex

```

SCATrEx uses [JAX](https://github.com/google/jax) to perform automatic differentiation. By default, SCATrEx installs the CPU-only version of JAX, but we strongly recommend the use of GPU acceleration. Please follow the instructions in https://github.com/google/jax#pip-installation-gpu-cuda to install the GPU version of JAX.

## Preprint

https://doi.org/10.1101/2021.11.04.467244