Xingjie Pan's repositories
cylinder_fitting
Fit a set of 3D points to a cylinder surface.
MERFISH_probe_design
A python3 pipeline for MERFISH probe design.
pymol_scripts
Some helpful pymol scripts
pyrosetta_pymol_interface
An interface for using PyRosetta via pymol
pyrosetta_scripts
pyrosetta scripts
MERFISH_analysis
Scripts for MERFISH data analysis.
abc_atlas_access
Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
MERlin
MERFISH decoding software
simple_biophysics_models
Biophysics models that are simple but helpful.
storm-control
Microscope control software
forward_folding
ab inito protein structure prediction
high-dim_points_geometric_analysis
Analyze geometric properties of points in a high dimensional space.
linker_loop_database
Scripts to make databases of loops that connect secondary structure elements
pdbGrafter
pdbGrafter grafts parts of a set of structures to another set of structures
ScientificProjectManager
ScientificProjectManager provides a paradigm along with a set of tools to make a scientific project organized and efficient.
ss_generator
Generate protein secondray structure backbones from a set of geometric parameters
structure_relax
Exploring the near minima protein free energy landscape