https://github.com/cbg-ethz/scdna-pipe

Python data analysis pipeline for single cell copy number event history reconstruction
https://github.com/cbg-ethz/scdna-pipe

bioinformatics bioinformatics-pipeline data-analysis genomics python snakemake snakemake-workflows workflow

Last synced: 5 months ago
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Python data analysis pipeline for single cell copy number event history reconstruction

• Host: GitHub
• URL: https://github.com/cbg-ethz/scdna-pipe
• Owner: cbg-ethz
• License: apache-2.0
• Created: 2019-11-14T16:14:41.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-05-29T12:57:27.000Z (about 2 years ago)
• Last Synced: 2025-01-28T02:42:46.476Z (over 1 year ago)
• Topics: bioinformatics, bioinformatics-pipeline, data-analysis, genomics, python, snakemake, snakemake-workflows, workflow
• Language: Python
• Homepage:
• Size: 16.8 MB
• Stars: 2
• Watchers: 4
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Single-cell DNA Analysis 

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## About

Reproducible Python pipeline for genomic data analysis. Performs single-cell copy number variation calling by learning the underlying tumour evolution history by state-of-the-art phylogenetic tree reconstruction method: SCICoNE. The pipeline is built using Python, Conda environment management system and the Snakemake workflow management system. The pipeline starts from the raw sequencing files and a settings file for the parameter configurations. After the analysis, it produces a report and multiple figures to inform the treatment decision of the cancer patient.

The pipeline makes use of `scgenpy`, a package that exposes functions for preprocessing, postprocessing and plotting data, allowing you to interact with data outside the pipeline context.

## Installing

1. Clone the repository

2. Install and update using `pip`:

  ```bash

  pip install -e .

  ```

3. Install SCICoNE.

## Running

1. Prepare the configuration file according to your analysis

2. Run `snakemake` with:

  ```bash

  snakemake --configfile your_config_file

  ```

3. (Optional) Refer to https://snakemake.readthedocs.io to customise your `snakemake` for your environment

## Contributing

You are very welcome to contribute! You can start with the existing issues or create new issues.

Make sure to follow the CI checks. Use the [pre-commit hook](https://github.com/cbg-ethz/scdna-pipe/blob/master/.pre-commit-config.yaml) defined in the project to meet the code style. If you are adding new functionality, add the corresponding test as well in order to keep the code coverage high.

## License

This project is licensed under the Apache License - see the [LICENSE](LICENSE) file for details