My professional repository of project and publication data files in computational biology and data science.
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Updated
Jul 16, 2024
My professional repository of project and publication data files in computational biology and data science.
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
An interoperable Python framework for biomolecular simulation.
Awesome list of computational biology.
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
UCSC Genome Browser source tree. Stable branch: "beta".
Mathematical Modeling for Systems Biology
Implementation of DiffDock-Pocket: Diffusion for Pocket-Level Docking with Side Chain Flexibility
Website for Mangul Lab.
A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).
DANCE: a deep learning library and benchmark platform for single-cell analysis
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
Infectious Disease Sequencing Platform
All UCSC Genome Browser source code that is under an open source license, mostly file format converters, command line tools and C libraries. A subset of the "kent" repo, updated every three weeks.
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
Implementations of various simulations for integrate and fire models, as well as conductance based models with synaptic neurotransmission
WebGL accelerated JavaScript molecular graphics library
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
Interactive network visualization in Python and Dash, powered by Cytoscape.js
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