Python package to query cancer variant databases
- Free software: MIT license
- Documentation: https://querynator.readthedocs.io.
- Command-line tool to query the cancergenomeinterpreter via its REST API
- Command-line tool to query the Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase using CIViCpy
This package uses the cancergenomeinterpreter.org REST API for data retrieval.
- Muiños, F., Martínez-Jiménez, F., Pich, O. et al. In silico saturation mutagenesis of cancer genes. Nature 596, 428–432 (2021). https://doi.org/10.1038/s41586-021-03771-1
- Tamborero, D. Rubio-Perez, C., Deu-Pons, J. et al., Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations. Genome Medicine 10, (2018). doi: https://doi.org/10.1101/140475
This package uses the CIViCpy package for data retrieval from the CIViC database.
- Wagner, Alex H., et al. "CIViCpy: a python software development and analysis toolkit for the CIViC knowledgebase." JCO Clinical Cancer Informatics 4 (2020): 245-253. doi: https://doi.org/10.1200/CCI.19.00127
- Griffith, M., Spies, N., Krysiak, K. et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet 49, 170–174 (2017). doi: https://doi.org/10.1038/ng.3774
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.