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    • gerlib

      Public
      A library of general-purpose tools, typically for processing or analysis of data from a sequencing and/or imaging experiment
      Scala
      1090Updated Feb 9, 2026Feb 9, 2026
    • Custom jupyterlab build for CLIP HPC with necessary packages installed
      Shell
      5000Updated Feb 3, 2026Feb 3, 2026
    • scsHi-C preprocessing Nextflow pipeline
      Groovy
      0500Updated Jan 23, 2026Jan 23, 2026
    • Visualisation (in `napari`) of nuclei from looptrace
      Python
      1120Updated Nov 4, 2025Nov 4, 2025
    • A `napari` plugin to facilitate interactive viewing of regional barcode spots from `looptrace`
      Python
      0070Updated Nov 4, 2025Nov 4, 2025
    • Visualisation (in `napari`) of locus-specific spots from looptrace
      Python
      1150Updated Nov 4, 2025Nov 4, 2025
    • gertils

      Public
      general GERlich group uTILitieS
      Python
      11120Updated Nov 4, 2025Nov 4, 2025
    • Finding FISH spots
      Python
      11100Updated Nov 3, 2025Nov 3, 2025
    • illumifix

      Public
      Correction of uneven illumination across a field of view
      Python
      1000Updated Oct 31, 2025Oct 31, 2025
    • Base container preinstalling all internally used NGS and image analysis tools.
      Python
      1110Updated Oct 3, 2025Oct 3, 2025
    • Extension of pore-c snakemake pipeline to include BrdU detection and sister chromatid discrimination
      Python
      16010Updated Oct 3, 2025Oct 3, 2025
    • Main container for gerlichlab/sister-pore-c-snakemake
      Dockerfile
      0000Updated Oct 3, 2025Oct 3, 2025
    • Code used in Teloni et al.
      Jupyter Notebook
      0100Updated Oct 3, 2025Oct 3, 2025
    • reparafil

      Public
      Analysis of DNA double-strand break (DSB) repair, especially as by homologous recombination (HR)
      Scala
      0190Updated Oct 2, 2025Oct 2, 2025
    • linescan

      Public
      A tool that does a linescan and performs peak detection and alignment based on FIJI ROIs.
      Python
      0000Updated Aug 18, 2025Aug 18, 2025
    • Custom jupyterlab build for CLIP HPC
      Shell
      5000Updated Feb 21, 2025Feb 21, 2025
    • DNAscent

      Public
      Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
      C++
      15000Updated Dec 19, 2024Dec 19, 2024
    • Docker wrapper for DNAscent
      Dockerfile
      0000Updated May 6, 2024May 6, 2024
    • A set of type stubs for popular Python packages. These are works in progress from the Microsoft Python team and others, with the intent that they are contribute…
      Python
      104100Updated Apr 18, 2024Apr 18, 2024
    • tracebot

      Public
      Clone of this project Ellenberg Lab (EMBL)
      Python
      0000Updated Apr 16, 2024Apr 16, 2024
    • A visual exploration and hypothesis testing tool for 3D genomics
      Python
      21390Updated Apr 12, 2024Apr 12, 2024
    • spoc

      Public
      Python
      0501Updated Apr 2, 2024Apr 2, 2024
    • Tool to preprocess data and upload it to a HiGlass instance
      Python
      0000Updated Nov 3, 2023Nov 3, 2023
    • Code used in Batty et al.
      Jupyter Notebook
      0100Updated Jun 26, 2023Jun 26, 2023
    • HiCognition library and CLI tool
      Python
      0100Updated Dec 14, 2022Dec 14, 2022
    • dash app for exploring higher order triplet contacts
      Python
      0000Updated Oct 13, 2022Oct 13, 2022
    • FIJI scripts used in Schneider et al. Nature (2022)
      ImageJ Macro
      0000Updated May 25, 2022May 25, 2022
    • fguard

      Public
      Python
      0000Updated Mar 3, 2022Mar 3, 2022
    • repo for github pages
      0000Updated Feb 21, 2022Feb 21, 2022
    • ngs

      Public
      A collections of functions to facilitate analysis of HiC data based on the cooler and cooltools interfaces.
      Python
      0610Updated Jan 21, 2022Jan 21, 2022