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Alireza Tafazzol (Ali)'s Projects

amberutils icon amberutils

Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods

bio3d icon bio3d

A mirror of official bio3d development site at Bitbucket: https://bitbucket.org/Grantlab/bio3d. See also bio3d website: http://thegrantlab.org/bio3d

caret icon caret

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models

cnmf icon cnmf

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

cnmf_ icon cnmf_

Packaged implementation of consensus nonnegative matrix factorization (cNMF; Kotliar, et al. 2019) for single-cell data analysis

cpptraj icon cpptraj

Biomolecular simulation trajectory/data analysis.

mmgbsa icon mmgbsa

Some code to extract data from Amber 15 MMGBSA.py output

mmpbsa icon mmpbsa

MMPBSA Free Energy Calculation Program

msmbuilder icon msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

nmf icon nmf

NMF: A Flexible R package for Nonnegative Matrix Factorization

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