Ultra fast chromosome 3D reconstraction.

Project description

NucBox

Ultra fast chromosome 3D reconstraction.

Install from source:

$ git clone https://github.com/Nanguage/NucBox.git
$ cd NucBox
$ pip install -e .

Reconstruct genome using Nuc Dynamics algorithm:

$ python -m nucbox.simu.nucdyn --arch=cuda ./cell1.pairs.gz ./out1.csv --use-grid=True --scale=0.01

Visualize the reconstructed genome:

$ python -m nucbox.gui.browser ./out1.csv

Convert the particles csv file to pdb file(for visualization in pymol or vmd):

$ python -m nucbox.utils.io particles_to_pdb ./out1.csv ./out1.pdb --split-by-chrom=True

This version

0.1.1

Mar 30, 2024

0.1.0

Mar 23, 2024

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Uploaded Mar 30, 2024 Source

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