Repositories list

• discrete-time-extrusion

  Public
  ReScript

  •

  MIT License

  •0•0•1•0•Updated Jan 29, 2025Jan 29, 2025

• chromoscores

  Public
  can start putting some scores here, perhaps divided into contactscores and distancescores to begin

  Jupyter Notebook

  •

  The Unlicense

  •2•1•4•0•Updated Jan 21, 2025Jan 21, 2025

• fastaFRiP

  Public
  pipeline for calculating FRiP from fasta (or bed + fasta)

  Python

  •0•2•2•1•Updated Jan 9, 2025Jan 9, 2025

• akitaV2-analyses

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

• DeepLearning_for_3DgenomeFoldingTutorial

  Public
  tutorial repository

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• dynamic_extrusion_boundaries

  Public
  Jupyter Notebook

  •

  MIT License

  •4•2•0•0•Updated Dec 10, 2024Dec 10, 2024

• 2024_seq-to-profile

  Public
  MIT License

  •1•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• dynamic_extrusion_boundaries_review

  Public
  Jupyter Notebook

  •

  MIT License

  •4•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• five_state_cohesin

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Sep 21, 2024Sep 21, 2024

• extrusion_with_dynamic_boundaries

  Public
  Jupyter Notebook

  •

  MIT License

  •4•0•0•0•Updated Aug 2, 2024Aug 2, 2024

• akita_utils

  Public
  utilities for use with Akita

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

• group-website

  Public
  TeX

  •

  MIT License

  •5•0•0•0•Updated Jun 27, 2024Jun 27, 2024

• chromoscores-update

  Public
  can start putting some scores here, perhaps divided into contactscores and distancescores to begin

  Jupyter Notebook

  •

  The Unlicense

  •2•0•0•0•Updated May 30, 2024May 30, 2024

• qbio577_fall2023

  Public
  Jupyter Notebook

  •

  MIT License

  •24•0•0•5•Updated Apr 23, 2024Apr 23, 2024

• bioframe

  Public
  Pandas utilities for tab-delimited and other genomic data files

  Python

  •

  MIT License

  •30•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• Loop_extrusion_velocity_chromosome

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 27, 2024Jan 27, 2024

• qbio577_fall2022

  Public
  Jupyter Notebook

  •

  MIT License

  •24•0•0•16•Updated Dec 5, 2023Dec 5, 2023

• 2023_seq-to-profile

  Public
  MIT License

  •1•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• higlass-python

  Public
  Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer

  Python

  •

  MIT License

  •12•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• transcription-modeling

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Feb 3, 2022Feb 3, 2022