https://github.com/cbg-ethz/scdna-pipe
Python data analysis pipeline for single cell copy number event history reconstruction
Science Score: 13.0%
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Low similarity (17.0%) to scientific vocabulary
Keywords
Repository
Python data analysis pipeline for single cell copy number event history reconstruction
Basic Info
Statistics
- Stars: 2
- Watchers: 4
- Forks: 0
- Open Issues: 3
- Releases: 1
Topics
Metadata Files
README.md
Single-cell DNA Analysis 
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
- Clone the repository
- Install and update using
pip:bash pip install -e . - Install SCICoNE.
Running
- Prepare the configuration file according to your analysis
- Run
snakemakewith:bash snakemake --configfile your_config_file - (Optional) Refer to https://snakemake.readthedocs.io to customise your
snakemakefor 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 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 file for details
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 9
- Total pull requests: 10
- Average time to close issues: 5 months
- Average time to close pull requests: 4 days
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 0.89
- Average comments per pull request: 0.3
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- pedrofale (6)
- monicadragan (1)
- anilbey (1)
Pull Request Authors
- pedrofale (7)
- monicadragan (3)