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bayesian_example

dpd_withremovingbonds

dpdchrom

Reconstruction of 3D conformation of chromatin fiber using single cell Hi-C data

dstmatrixfromlmpfile

Short script to create distance matrix in dat fromat from lmp file (LAMMPS).

dynamic_seq

Playground to study possible collective properties of sequences depending on the rules.

example_hmm

gdload

Download file from google drive in the terminal.

gen_init_conf_4_lammps

Generate initial conformation of a polymer chain for LAMMPS.

generate_mol2_topology

hic_subtraction

Hic matrix subtraction

hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

icd_coding_multi-filter-res-cnn

Multi-Filter Residual Convolutional Neural Network for Text Classification

lammps_le

Loop extrusion module with LAMMPS

lammpstrj_motion_correction

Subtract the translational and rotational movement of the polymer chain to study subdiffusion. It works quite bad for systems with less than 50 beads.

logbin

Logarithmic binning python script

loopextrusion

match_time_units_sim_exp

Match time units of simulations with the real time units (sec). We have the data from a cell line without additional CTCF site and cohesin.

mocca

Open-source Python project to analyze HPLC–DAD raw data.

simple_icd_10_gm

A simple python library for ICD-10-gm (german modification) codes

speed_up_msd

Here you can find a python script to reproduce all the plots from the medium article.

unpub_dpd_analysis