Check out our full GitHub repository here.

1. VAPr: a Python package for NoSQL variant data storage, annotation and prioritization

2. mali-dual-crispr-pipeline: code for the dual-CRISPR screen analysis pipeline developed to analyze results from the dual-CRISPR screening system set up by the lab of Dr. Prashant Mali. The software is developed by Amanda Birmingham and Roman Sasik of the Center for Computational Biology and Bioinformatics at the University of California, San Diego.

3. visJS2jupyter a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells

4. cmi_metadata_wizard: a web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints

5. jupyter-pathway: canonical pathway visualization and analysis

6. jupyter-genomics: a collection of Jupyter notebooks authored, including methods on utilizing cloud computing resources and analysis of data from next-generation sequencing, systems biology, and microbiome.


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