Name: Alireza Tafazzol (Ali)
Type: User
Company: UC Davis
Bio: A postdoc fellow at Genentech's oncology biomarker development (OBD), working on development of neoantigen cancer vaccines.
Computational Biology | Bioinfo
Blog: https://www.linkedin.com/in/tafazzol
Alireza Tafazzol (Ali)'s Projects
Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods
A mirror of official bio3d development site at Bitbucket: https://bitbucket.org/Grantlab/bio3d. See also bio3d website: http://thegrantlab.org/bio3d
caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Packaged implementation of consensus nonnegative matrix factorization (cNMF; Kotliar, et al. 2019) for single-cell data analysis
Biomolecular simulation trajectory/data analysis.
Some code to extract data from Amber 15 MMGBSA.py output
MMPBSA Free Energy Calculation Program
:building_construction: Statistical models for biomolecular dynamics :building_construction:
Data visualizations for biomolecular dynamics
NMF: A Flexible R package for Nonnegative Matrix Factorization
Python interface of cpptraj