- Coassin_pipeline's dependency is packaged in Coassin_pipeline/app_tar, for details, see the Readme file in Coassin_pipeline.
- The project's python dependencies and releases are managed by Poetry. If you only works on codes, related information can be found at pyproject.toml under section tool.poetry.dependencies, For running details, see the Readme file in src/lpa_pipeline.
- Some visualization code are written by R. The sessionInfo can be found at visualization/sessionInfo.txt
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Coassin_pipeline included shell script and all the related example file used running pipeline from Dr. Coassin et.al's paper A comprehensive map of single base polymorphisms in the hypervariable LPA Kringle-IV-2 copy number variation region, the pipeline is running on Cloudgene on a SGE or SLURM-managed cluster
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src/lpa_pipeline is the data analysis pipeline used in Python.
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METAL included the backup shell script running METAL 11.3.25 for meta analysis. These scripts are not required in the running
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For the VNTR estimating pipeline, please see the repo vntrwrap. Those pipeline are list separately for they are also working for other projects.
- Most of the Python codes are documented in their source code
- A copy of the sphinx-autoapi based doc can be found in docs/_build/html/index.html. Due to some version issue we cannot host it on readthedoc.
Those figure which readers might interested in but not related to the storytelling are included in other_figures
The repository was created by Yihao Li. It is licensed under the terms of the MIT license.
If need help or can help with anything, please feel free to email Yihao Li (yl4326@cumc.columbia.edu) and CC both Dr. Gissette Reyes-Soffer (gr2104@cumc.columbia.edu) and Dr. Badri Vardarajan (bnv2103@cumc.columbia.edu)