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    37 repositories

    • looptrace-loci-vis

      Public
      Visualisation (in `napari`) of locus-specific spots from looptrace
      Python
      •
      MIT License
      •1•1•5•0•Updated Oct 30, 2025Oct 30, 2025

    • spotfishing

      Public
      Finding FISH spots
      Python
      •
      MIT License
      •1•1•10•0•Updated Oct 29, 2025Oct 29, 2025

    • illumifix

      Public
      Correction of uneven illumination across a field of view
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 28, 2025Oct 28, 2025

    • gertils

      Public
      general GERlich group uTILitieS
      Python
      •
      MIT License
      •1•1•12•0•Updated Oct 28, 2025Oct 28, 2025

    • gerlich_jupyter

      Public
      Base container preinstalling all internally used NGS and image analysis tools.
      Python
      •
      MIT License
      •1•1•1•0•Updated Oct 3, 2025Oct 3, 2025

    • sister-pore-c-snakemake

      Public
      Extension of pore-c snakemake pipeline to include BrdU detection and sister chromatid discrimination
      Python
      •
      Other
      •15•0•1•0•Updated Oct 3, 2025Oct 3, 2025

    • sister-pore-c-docker

      Public
      Main container for gerlichlab/sister-pore-c-snakemake
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • teloni_et_al

      Public
      Code used in Teloni et al.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Oct 3, 2025Oct 3, 2025

    • reparafil

      Public
      Analysis of DNA double-strand break (DSB) repair, especially as by homologous recombination (HR)
      Scala
      •
      GNU General Public License v3.0
      •0•1•9•0•Updated Oct 2, 2025Oct 2, 2025

    • replchromconf-jupyterlab

      Public
      Custom jupyterlab build for CLIP HPC with necessary packages installed
      Shell
      •5•0•0•0•Updated Sep 30, 2025Sep 30, 2025

    • gerlib

      Public
      A library of general-purpose tools, typically for processing or analysis of data from a sequencing and/or imaging experiment
      Scala
      •
      Apache License 2.0
      •1•0•9•0•Updated Sep 9, 2025Sep 9, 2025

    • linescan

      Public
      A tool that does a linescan and performs peak detection and alignment based on FIJI ROIs.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

    • looptrace-regionals-vis

      Public
      A `napari` plugin to facilitate interactive viewing of regional barcode spots from `looptrace`
      Python
      •
      MIT License
      •0•0•7•0•Updated Jul 18, 2025Jul 18, 2025

    • nuclei-vis-napari

      Public
      Visualisation (in `napari`) of nuclei from looptrace
      Python
      •
      MIT License
      •1•1•2•0•Updated Apr 2, 2025Apr 2, 2025

    • clip-jupyterlab-minimal

      Public
      Custom jupyterlab build for CLIP HPC
      Shell
      •5•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • DNAscent

      Public
      Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
      C++
      •
      GNU General Public License v3.0
      •15•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • dnascent-docker

      Public
      Docker wrapper for DNAscent
      Dockerfile
      •0•0•0•0•Updated May 6, 2024May 6, 2024

    • python-type-stubs

      Public
      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 contributed to typeshed or to the associated packages once sufficiently complete.
      Python
      •
      MIT License
      •103•1•0•0•Updated Apr 18, 2024Apr 18, 2024

    • tracebot

      Public
      Clone of this project Ellenberg Lab (EMBL)
      Python
      •0•0•0•0•Updated Apr 16, 2024Apr 16, 2024

    • hicognition

      Public
      A visual exploration and hypothesis testing tool for 3D genomics
      Python
      •
      MIT License
      •2•13•9•0•Updated Apr 12, 2024Apr 12, 2024

    • spoc

      Public
      Python
      •
      MIT License
      •0•5•0•1•Updated Apr 2, 2024Apr 2, 2024

    • higlassupload

      Public
      Tool to preprocess data and upload it to a HiGlass instance
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2023Nov 3, 2023

    • Batty_et_al_EMBO.J_2023

      Public
      Code used in Batty et al.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 26, 2023Jun 26, 2023

    • hicognition_lib

      Public
      HiCognition library and CLI tool
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 14, 2022Dec 14, 2022

    • triplet-exploration

      Public
      dash app for exploring higher order triplet contacts
      Python
      •0•0•0•0•Updated Oct 13, 2022Oct 13, 2022

    • schneider_et_al_Nature_2022

      Public
      FIJI scripts used in Schneider et al. Nature (2022)
      ImageJ Macro
      •0•0•0•0•Updated May 25, 2022May 25, 2022

    • fguard

      Public
      Python
      •0•0•0•0•Updated Mar 3, 2022Mar 3, 2022

    • gerlichlab

      Public
      repo for github pages
      0•0•0•0•Updated 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
      •
      MIT License
      •0•6•1•0•Updated Jan 21, 2022Jan 21, 2022

    • scshic_docker

      Public
      Container with tools to analyse scsHi-C data.
      Dockerfile
      •1•0•0•0•Updated Nov 30, 2021Nov 30, 2021