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    43 repositories

    • Docker-Machines

      Public archive
      Docker Files and docker-compose files for various machines
      Shell
      •0•2•0•0•Updated Feb 20, 2026Feb 20, 2026

    • labsite

      Public
      Lab website built using static site generation
      Nunjucks
      •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • unionloops-nf

      Public
      A HiCCUPS-based pipeline for simultaneous chromatin loop calling and cross-sample comparison, where both steps reinforce each other.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • unionloops_paper

      Public
      Scripts and notebooks used in Liu et al. paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • Flagship_paper

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

    • Ozgun-ALS

      Public
      ALS paper
      Jupyter Notebook
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • top2bko_atra_project

      Public
      Hi-C analysis for TOP2B KO in SH-SY5Y cells with ATRA treatment project
      Jupyter Notebook
      •2•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • inherited-folding-programs

      Public
      Jupyter Notebook
      •2•2•0•0•Updated Oct 9, 2024Oct 9, 2024

    • cLIMS-docker

      Public
      cLIMS repository running on Docker Contaienrs
      Python
      •
      GNU Lesser General Public License v3.0
      •4•3•23•3•Updated Sep 27, 2024Sep 27, 2024

    • Topo-II-Inhibition-Manuscript

      Public
      Github Repo for Hi-C and MC-3C analysis scripts for the Topo II Inhibition Manuscript
      hicmc3c
      hicmc3c
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Feb 3, 2024Feb 3, 2024

    • pita_project

      Public
      hi-c related analysis for the PITA-project
      Jupyter Notebook
      •0•2•0•0•Updated Dec 20, 2023Dec 20, 2023

    • distiller-nf

      Public
      a modular Hi-C mapping pipeline
      Groovy
      •
      MIT License
      •26•0•0•1•Updated Jul 12, 2023Jul 12, 2023

    • Single_cell_scripts

      Public
      Xiangru's scripts and notebooks for single-cell
      Shell
      •0•1•0•0•Updated Feb 16, 2023Feb 16, 2023

    • Zagelbaum_etal_NSMB_2022

      Public
      Notebooks for Hi-C analyses related to "Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin pol…
      Jupyter Notebook
      •0•4•1•0•Updated Oct 31, 2022Oct 31, 2022

    • ALV-repo

      Public
      Scripts and notebooks for ALV's publication
      Jupyter Notebook
      •
      MIT License
      •1•3•2•0•Updated Apr 21, 2022Apr 21, 2022

    • chimera-tie-public

      Public
      a split-read alignment process for mapping multi-chimeric reads
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Aug 3, 2021Aug 3, 2021

    • matrix_shared

      Public
      collection of scripts, config files and other materials related to the Matrix project
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Mar 31, 2021Mar 31, 2021

    • cooltools

      Public
      The tools for your .cool's
      Python
      •
      MIT License
      •55•4•0•0•Updated Feb 26, 2021Feb 26, 2021

    • matrix_paper

      Public
      Scripts and notebooks used in Akgol Oksuz et al. paper
      Jupyter Notebook
      •1•11•1•0•Updated Jan 18, 2021Jan 18, 2021

    • chimera-tie

      Public
      a split-read alignment process for mapping multi-chimeric reads
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 7, 2021Jan 7, 2021

    • digest-Hi-C

      Public
      R
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Sep 4, 2020Sep 4, 2020

    • allelic-rt-supplement

      Public
      supplementary analysis for the allelic RT study
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 10, 2020Aug 10, 2020

    • experimental

      Public
      some experimental notebooks
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 3, 2020Jun 3, 2020

    • psb-sysbio-course-hic-part

      Public
      Systems Biology Course matlab session
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2020Apr 14, 2020

    • MC-3C_scripts

      Public
      Scripts used to process and analyse the data in the MC-3C paper
      R
      •2•2•1•0•Updated Mar 11, 2020Mar 11, 2020

    • snakedots

      Public
      little snakemake pipeline to call dots with re-balanced coolers
      Python
      •
      MIT License
      •0•0•3•0•Updated Mar 7, 2020Mar 7, 2020

    • higlass-manage

      Public
      A utility script to manage local docker instances of HiGlass
      Python
      •
      MIT License
      •9•0•0•0•Updated Jan 23, 2020Jan 23, 2020

    • DNATriangulation

      Public
      A set of scripts for genome assembly
      Python
      •1•0•3•0•Updated Dec 30, 2019Dec 30, 2019

    • Abramo_2019

      Public
      some scripts and notebooks for the Abramo et al 2019 paper
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Oct 25, 2019Oct 25, 2019

    • renseq

      Public
      Renseq Pacbio pipeline
      Shell
      •2•1•0•0•Updated Sep 17, 2019Sep 17, 2019
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