Tools and software created by CCBB:
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.
Check out our full GitHub repository here.
Community open source tools:
1. Cytoscape: an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
2. GenePattern: provides hundreds of analytical tools for the analysis of gene expression, sequence variation and copy number, proteomic, flow cytometry, and network analysis.
3. NDEx: an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge.