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    39 repositories

    • scshic_pipeline

      Public
      scsHi-C preprocessing Nextflow pipeline
      Groovy
      •
      MIT License
      •0•5•0•0•Updated Jul 15, 2026Jul 15, 2026

    • takacs_mylarshchikov_et_al

      Public
      Analysis code for Takacs, Mylarshchikov et al.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • 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•1•9•0•Updated Jul 7, 2026Jul 7, 2026

    • looptrace-regionals-vis

      Public
      A `napari` plugin to facilitate interactive viewing of regional barcode spots from `looptrace`
      Python
      •
      MIT License
      •0•1•8•0•Updated Apr 19, 2026Apr 19, 2026

    • replchromconf-jupyterlab

      Public
      JupyterLab image to process, analyze, and visualize data from Takacs, Mylarshchikov et al.
      Shell
      •5•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • peakflow

      Public
      A simple nextflow pipeline for calling peaks and producing tracks from ChIP-seq data
      nextflowbigwigchip-seq
      nextflowbigwigchip-seqmacs2peak-callingdeeptools
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • nuclei-vis-napari

      Public
      Visualisation (in `napari`) of nuclei from looptrace
      Python
      •
      MIT License
      •1•2•2•0•Updated Nov 4, 2025Nov 4, 2025

    • looptrace-loci-vis

      Public
      Visualisation (in `napari`) of locus-specific spots from looptrace
      Python
      •
      MIT License
      •1•2•5•0•Updated Nov 4, 2025Nov 4, 2025

    • gertils

      Public
      general GERlich group uTILitieS
      Python
      •
      MIT License
      •1•2•12•0•Updated Nov 4, 2025Nov 4, 2025

    • spotfishing

      Public
      Finding FISH spots
      Python
      •
      MIT License
      •1•1•10•0•Updated Nov 3, 2025Nov 3, 2025

    • illumifix

      Public
      Correction of uneven illumination across a field of view
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • gerlich_jupyter

      Public
      Base container preinstalling all internally used NGS and image analysis tools.
      Python
      •
      MIT License
      •1•2•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
      •16•1•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

    • 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

    • 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
      •16•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 contribute…
      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
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