mirnylab

Repositories

bioframe

Pandas utilities for tab-delimited and other genomic data files

Python MIT 9 18 18 0 Updated Aug 3, 2020

distiller-nf

a modular Hi-C mapping pipeline

Groovy MIT 13 33 48 (1 issue needs help) 2 Updated Jul 31, 2020

cooler

A cool place to store your Hi-C

python bioinformatics genomics file-format contact-matrix hdf5 sparse

Python BSD-3-Clause 34 98 26 (2 issues need help) 0 Updated Jul 18, 2020

polychrom

A new version of openmm-polymer

Python MIT 6 12 2 (1 issue needs help) 0 Updated Jul 16, 2020

cooltools

The tools for your .cool's

Python MIT 24 36 39 (1 issue needs help) 5 Updated Jul 8, 2020

one_sided_extrusion

Codes relevant for "Chromosome organization by one-sided and two-sided loop extrusion"

Jupyter Notebook MIT 1 2 0 0 Updated Jun 14, 2020

pairtools

CLI tools to process mapped Hi-C data

Python MIT 14 26 30 1 Updated May 13, 2020

cont3d

Utilities for working with 3-point contact matrices

Python 2 1 0 0 Updated Apr 20, 2020

pairlib

Read, write and analyse Hi-C pairs

Python MIT 0 0 2 0 Updated Mar 19, 2020

hiclib-legacy

A legacy repository. Was replaced by distiller, cooler, and cooltools.

Python MIT 0 3 0 0 Updated Mar 4, 2020

nglutils

Utility module for using nglview to visualize stuff

Python MIT 2 0 2 0 Updated Feb 20, 2020

mirnylib-legacy

A legacy repository. Useful functionality was ported to cooltools.lib.numutils.

Python MIT 0 1 0 0 Updated Feb 17, 2020

openmm-polymer-legacy

A legacy repository. Was replaced by polychrom.

HTML MIT 1 0 0 0 Updated Feb 17, 2020

GSG_mitotic_models_2018

Jupyter Notebook MIT 0 1 0 0 Updated May 10, 2019

cooler-binder

Cooler demo using a Jupyter notebook Binder

Jupyter Notebook 4 6 1 0 Updated Feb 23, 2019

pdSim

Gillespie simulations of advantageous drivers & deleterious passengers in cancer

cython python3 population-genetics gillespie-algorithm cancer-evolution

C MIT 0 0 0 0 Updated Feb 4, 2019

pyfilesplit

Python MIT 0 0 0 0 Updated Dec 21, 2018

distiller-test-data

Test data for distiller

Shell MIT 0 0 0 0 Updated Jul 19, 2018

pairsamtools

a legacy repo to avoid breaking existing pipelines

Python MIT 1 1 0 0 Updated Jul 18, 2018

distiller-sm

a Snakemake version of distiller (deprecated!)

Python MIT 2 0 8 0 Updated Apr 24, 2017