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@fmi-basel Friedrich Miescher Institute for Biomedical Research

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    99 repositories

    • faim-jetraw

      Public
      Python
      •
      Apache License 2.0
      •0•0•3•1•Updated Apr 27, 2026Apr 27, 2026

    • compbio-nomeR

      Public
      C++
      •
      Other
      •0•0•0•0•Updated Apr 19, 2026Apr 19, 2026

    • gbuehler-MiniChip

      Public
      small collection of R functions for ChIPseq analysis
      HTML
      •1•3•0•0•Updated Apr 17, 2026Apr 17, 2026

    • labbook-explog-fmi

      Public
      Obsidian plugin
      TypeScript
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • CaImagingTest

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • balance-controlled-plasticity

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated Apr 9, 2026Apr 9, 2026

    • faim-robocopy

      Public
      A python-based UI for robocopy
      Python
      •
      MIT License
      •0•4•6•1•Updated Apr 6, 2026Apr 6, 2026

    • FMI_H3.4

      Public
      Scripts used for the H3.4 manuscript
      C
      •0•0•1•0•Updated Mar 24, 2026Mar 24, 2026

    • sam_trainer

      Public
      A small package for augmenting images and training micro-sam models
      Python
      •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • Dreamer-CDP

      Public
      Python
      •
      MIT License
      •524•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • ggrossha_SWI

      Public template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•18•1•Updated Mar 19, 2026Mar 19, 2026

    • gpeters-fetchNOMe

      Public
      R package for fetching NOMe-seq data from BAM files
      C++
      •
      Other
      •0•0•0•1•Updated Feb 27, 2026Feb 27, 2026

    • ripple-detection

      Public
      0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • gliberal-scMultipleX

      Public
      Feature extraction and linking of multiplexing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•14•21•2•Updated Feb 10, 2026Feb 10, 2026

    • stork

      Public
      A differentiable spiking neural network simulator
      Python
      •
      MIT License
      •4•25•0•0•Updated Dec 5, 2025Dec 5, 2025

    • recurrent-predictive-learning

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 25, 2025Nov 25, 2025

    • Deep-learning-bZIPs

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2025Nov 8, 2025

    • au-smfish-flow

      Public
      Batch smFISH pipeline for MIP-based cell/nucleus segmentation (Cellpose), spot detection (big-fish), SNR filtering, per-cell nuc/cyto counts; outputs AnnData, C…
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • gfelsenb-2p-analysis-warnecke-2025

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • spiking-sqp

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 29, 2025Sep 29, 2025

    • gmatthia_mg132-timecourse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • ggrossha-ce-chromatin-oscillations-TF-modelling

      Public
      R
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • RosEM

      Public
      Pipeline and GUI for cryoEM model refinement using Rosetta and Phenix
      guirefinementmodelling
      guirefinementmodellingrosettaphenixcryoem
      Python
      •
      Apache License 2.0
      •1•2•0•0•Updated Aug 8, 2025Aug 8, 2025

    • gfriedri-brainmaps-api

      Public
      Python
      •1•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • gthoma_rosetta-density-crosslink-docking

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • gthoma_scan-factor

      Public
      PyMOL plugin to move a probe DNA (e.g. TF bound to free DNA) along a target DNA (e.g. nucleosome) and calculate clashes
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • 1Photon_Analysis

      Public
      This repository is a streamlined Miniscope Analysis pipeline that utilizes open source projects to motion correct, extract curate and align Miniscope data.
      matlabcalcium-imagingminiscope-imaging
      matlabcalcium-imagingminiscope-imaging
      MATLAB
      •
      MIT License
      •2•2•0•0•Updated May 16, 2025May 16, 2025

    • 2Photon_Analysis

      Public
      This repository is a streamlined Two-Photon Imaging pipeline that utilizes open source projects to motion correct, extract and curate data collected with a Bruk…
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • neuRoi

      Public
      MATLAB
      •5•1•7•0•Updated Apr 19, 2025Apr 19, 2025

    • gfelsenb-fictrac

      Public
      FicTrac: A webcam-based method for tracking spherical motion and generating fictive animal paths. This is a fork to make installation work on new Windows 11 mac…
      C++
      •
      Other
      •38•0•0•0•Updated Apr 11, 2025Apr 11, 2025
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