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    16 repositories

    • DHPSFU_Fiji_Plugin

      Public
      Roff
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • DHPSFU

      Public
      Python
      •0•1•0•0•Updated May 14, 2025May 14, 2025

    • formative-state-analysis

      Public
      R
      •0•1•0•0•Updated Feb 9, 2023Feb 9, 2023

    • DFT-drift-correction

      Public
      MATLAB
      •0•0•0•0•Updated Dec 24, 2021Dec 24, 2021

    • nuc_processing

      Public
      Chromatin contact paired-read single-cell Hi-C processing module for Nuc3D and NucTools
      Python
      •
      GNU Lesser General Public License v3.0
      •10•7•0•0•Updated Apr 6, 2018Apr 6, 2018

    • point-alignment

      Public
      Python (partial) coherent point drift implementation
      Python
      •5•1•0•0•Updated Jan 17, 2018Jan 17, 2018

    • nuc_dynamics

      Public
      Particle dynamics and simulated annealing for chromosome structure calculation
      Python
      •11•18•0•0•Updated Jan 17, 2018Jan 17, 2018

    • trajectory-analysis

      Public
      Python
      •0•0•0•0•Updated Oct 18, 2017Oct 18, 2017

    • nuc_frames

      Public
      Utilities to help with analysing distances and depths in multiple single-cell Hi-C genome structures.
      Python
      •1•1•0•0•Updated Jul 5, 2017Jul 5, 2017

    • weimann-tracking

      Public
      MATLAB single molecule tracking (adapted from Weimann et al 2013)
      MATLAB
      •0•0•0•0•Updated Jun 7, 2017Jun 7, 2017

    • tiffutil

      Public
      Python scripts for working with TIFF stacks
      Python
      •1•0•0•0•Updated Apr 25, 2017Apr 25, 2017

    • blob-detection

      Public
      Python nD laplacian-of-gaussian blob detection
      Python
      •10•4•0•0•Updated Apr 25, 2017Apr 25, 2017

    • blink-analysis

      Public
      Analysis of blinking spots for FRET paper
      Python
      •2•0•0•0•Updated Apr 24, 2017Apr 24, 2017

    • gene-depth

      Public
      Python scripts for calculating depths of peaks in background segments
      Python
      •2•0•0•0•Updated Jan 17, 2017Jan 17, 2017

    • single_cell_loop_analysis

      Public
      Jupyter notebooks analysing potential loop interactions (e.g. Cohesin/CTCF) in single cell Hi-C genome structures.
      Jupyter Notebook
      •1•1•0•0•Updated Sep 27, 2016Sep 27, 2016

    • genome_structure_analysis

      Public
      Analysis code for population and single-cell Hi-C data. Includes functions for calculating "Void" regions, "A/B" compartments and spatial density enrichment.
      Jupyter Notebook
      •2•7•0•0•Updated Jul 15, 2016Jul 15, 2016
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