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    13 repositories

    • Harabula_Speakman_Superenhancer_networks_2025

      Public
      This repository contains pipelines and code for the manuscrupt "Specialised super-enhancer networks in stem cells and neurons""
      Python
      •1•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • Vojtasova_Righelli_2025_HITs-and-SWINGs

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • GAM_phaser

      Public
      Perl
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • multiplex-gam-2023

      Public
      Analysis scripts for Multiplex-GAM paper (Beagrie, Thieme, Annunziatella et al. 2023)
      Jupyter Notebook
      •1•4•1•0•Updated Jun 24, 2024Jun 24, 2024

    • Irastorza-Azcarate_Kukalev_Kempfer_2024

      Public
      Code used to plot the figures in "Extensive folding variability between homologous chromosomes in mammalian cells"
      Python
      •1•0•0•0•Updated May 29, 2024May 29, 2024

    • MELTRONIC

      Public
      Detection of chromatin melting and condensation events in regions of interest from GAM data
      R
      •
      MIT License
      •1•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • 3DOmics

      Public
      Shell
      •0•1•0•0•Updated Aug 29, 2023Aug 29, 2023

    • gamtools

      Public
      Processing, quality control and analysis of GAM datsets
      pythonpython3python2high-throughput-sequencingmolecular-biologychromatin
      Python
      •
      Apache License 2.0
      •14•9•7•4•Updated Jun 13, 2023Jun 13, 2023

    • gamtools-guix

      Public
      Guix channel definition for gamtools
      Scheme
      •1•1•0•0•Updated Oct 28, 2022Oct 28, 2022

    • WinickNg_Kukalev_Harabula_Nature_2021

      Public
      Collection of supplementary data and code for the publication W. Winick-Ng, A. Kukalev, I. Harabula "Cell-type specialization is encoded by specific chromatin topologies" (2021) Nature
      Python
      •1•4•0•0•Updated May 16, 2022May 16, 2022

    • 4DN_JAWG_H1

      Public
      R
      •1•0•0•0•Updated Jan 13, 2022Jan 13, 2022

    • GAM_trans_cis_ratio

      Public
      Calculation of trans-cis NPMI ratios from GAM data
      R
      •
      MIT License
      •1•1•0•0•Updated Nov 26, 2021Nov 26, 2021

    • Meltron

      Public
      a statistical framework to detect differences in chromatin contact density at genomic regions of interest
      R
      •
      MIT License
      •1•4•0•0•Updated Nov 26, 2021Nov 26, 2021