mirnylab/microcompartments

Polymer simulations of compartments and extrusion modeling the mitosis-to-G1 transition

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mirnylab/Hi-C_Workshop

Materials for the workshop at Genome Architecture and Function 2024 Workshop

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mirnylab/one_sided_extrusion

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

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mirnylab/pdSim

Gillespie simulations of advantageous drivers & deleterious passengers in cancer

Language: C - Size: 860 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

mirnylab/openmm-polymer-legacy

A legacy repository. Was replaced by polychrom.

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mirnylab/hiclib-legacy

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

Language: Python - Size: 43.2 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 15 - Forks: 5

mirnylab/GenomeArchitectureAndFunction2023

Materials for the workshop at Genome Architecture and Function 2023 Workshop

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mirnylab/chicken2.0_paper

Repository for analysis code related to Chicken2.0

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mirnylab/heterochromatin-paper

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mirnylab/mirnylib-legacy

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

Language: Python - Size: 7.11 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

mirnylab/MCMs-as-random-barriers-to-loop-extrusion-paper

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mirnylab/moving-barriers-paper

Simulation and analysis codes used in Banigan*, Tang*, van den Berg* et al. Transcription shapes 3D chromatin organization by interacting with loop-extruding cohesin complexes, bioRxiv (2021)

Language: Python - Size: 41 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

mirnylab/nglutils

Utility module for using nglview to visualize stuff

Language: Python - Size: 682 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

mirnylab/Open2C

Community software repositories (cooler, cooltools, pairtools, distiller, polychrom, bioframe, and others) now live at https://github.com/open2c

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mirnylab/TMB_analysis

R code and data for "Limited evidence of tumour mutational burden as a biomarker of response to immunotherapy", C Gurjao et al., 2020

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mirnylab/cont3d

Utilities for working with 3-point contact matrices

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mirnylab/GSG_mitotic_models_2018

Language: Jupyter Notebook - Size: 366 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

mirnylab/pairsamtools

a legacy repo to avoid breaking existing pipelines

Language: Python - Size: 693 KB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 1