mirnylab

hiclib-legacy

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

GenomeArchitectureAndFunction2023

Materials for the workshop at Genome Architecture and Function 2023 Workshop

heterochromatin-paper

one_sided_extrusion

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

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

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

mirnylib-legacy

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

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)

cont3d

Utilities for working with 3-point contact matrices

nglutils

Utility module for using nglview to visualize stuff

GSG_mitotic_models_2018

Open2C

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

openmm-polymer-legacy

A legacy repository. Was replaced by polychrom.

pairsamtools

a legacy repo to avoid breaking existing pipelines

pdSim

Gillespie simulations of advantageous drivers & deleterious passengers in cancer

chicken2.0_paper

Repository for analysis code related to Chicken2.0

GenomeArchitectureAndFunction2024

Materials for the workshop at Genome Architecture and Function 2024 Workshop