OpenMiChroM
v1.0.6
Getting Started
Installation
Introduction
Open-MiChroM Modules
OpenMiChroM
Tutorials
Single Chromosome Simulation
Multiple Chromosome Simulation
Tutorial: Single chromosome optimization using OpenMiChroM
Tutorial: Full Inversion Method for a single chromosome using OpenMiChroM
Reference
How to cite
OpenMiChroM
References
License
OpenMiChroM
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Table of Contents
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Getting Started
Installation
Install via conda
Install via pip
Introduction
Open-MiChroM Modules
OpenMiChroM
OpenMiChroM.ChromDynamics
OpenMiChroM.Optimization
OpenMiChroM.CndbTools
Tutorials
Single Chromosome Simulation
Chromatin Dynamics Simulations on Chromosome 10 of GM12878 Cell Line
Trajectory analysis using cndbTools
Multiple Chromosome Simulation
Chromatin Dynamics Simulations on Chromosome 10 and Chromosome 11 of GM12878 Cell Line
Tutorial: Single chromosome optimization using OpenMiChroM
This tutorial enables performing optimization in MiChroM Parameters (Second-order optimization -> Hessian inversion)
Tutorial: Full Inversion Method for a single chromosome using OpenMiChroM
This tutorial enables performing Full Inversion Method using Adam (First-order optimization)
Fixing values on the force field
Reference
How to cite
OpenMiChroM
References
License
Indices and tables
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Index
Module Index
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