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@fmi-basel Friedrich Miescher Institute for Biomedical Research

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    87 repositories

    • gliberal-scMultipleX

      Public
      Feature extraction and linking of multiplexing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•9•20•1•Updated Aug 12, 2025Aug 12, 2025

    • faim-jetraw

      Public
      Python
      •
      Apache License 2.0
      •0•0•3•1•Updated Aug 11, 2025Aug 11, 2025

    • RosEM

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

    • faim-robocopy

      Public
      A python-based UI for robocopy
      Python
      •
      MIT License
      •0•3•6•1•Updated Aug 4, 2025Aug 4, 2025

    • balance-controlled-plasticity

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Jul 28, 2025Jul 28, 2025

    • gfriedri-brainmaps-api

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

    • labbook-explog-fmi

      Public
      Obsidian plugin
      TypeScript
      •0•0•0•0•Updated Jun 25, 2025Jun 25, 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

    • spiking-sqp

      Public
      MIT License
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • gbuehler-MiniChip

      Public
      small collection of R functions for ChIPseq analysis
      HTML
      •1•3•0•0•Updated May 22, 2025May 22, 2025

    • compbio-nomeR

      Public
      C++
      •
      Other
      •0•0•0•0•Updated May 19, 2025May 19, 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
      MATLAB
      •
      MIT License
      •1•1•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 Bruker 2Photon microscope.
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • gpeters-fetchNOMe

      Public
      R package for fetching NOMe-seq data from BAM files
      C++
      •
      Other
      •0•0•0•0•Updated May 7, 2025May 7, 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 machines with FLIR cameras (Spinnaker SDK).
      C++
      •
      Other
      •32•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • stork

      Public
      A differentiable spiking neural network simulator
      Python
      •
      MIT License
      •4•22•0•0•Updated Feb 10, 2025Feb 10, 2025

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

      Public
      R
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • faim-cryoflare

      Public
      CryoFLARE: FMI Live Analysis and Reconstruction Engine for single particle Cryo EM data
      C++
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Jan 27, 2025Jan 27, 2025

    • latent-predictive-learning

      Public
      Code to accompany our paper "The combination of Hebbian and predictive plasticity learns invariant object representations in deep sensory networks"
      deep-learningself-supervised-learninghebbian-plasticity
      Jupyter Notebook
      •
      MIT License
      •6•26•0•0•Updated Jan 14, 2025Jan 14, 2025

    • neural-decoding-RSNN

      Public
      Recurrent spiking neural networks (RSNNs) for decoding of motor signals from cortical spike trains
      Python
      •
      MIT License
      •5•10•0•0•Updated Jan 8, 2025Jan 8, 2025

    • surrogate-gradient-theory

      Public
      Jupyter Notebook
      •1•5•0•0•Updated Nov 22, 2024Nov 22, 2024

    • zarr_parallel_processing

      Public
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Nov 21, 2024Nov 21, 2024

    • ggiorget_ms2analysis

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • ggiorget_smFISH-Mobi-bursting

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • gfriedri_dataset-alignment

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•0•Updated Oct 8, 2024Oct 8, 2024

    • gfriedri-em-alignment-flows

      Public
      Python
      •
      Apache License 2.0
      •0•1•2•0•Updated Oct 4, 2024Oct 4, 2024

    • gfriedri-em-alignment

      Public
      Alignment tools used in the Friedrich lab.
      Python
      •
      Apache License 2.0
      •0•3•9•0•Updated Sep 10, 2024Sep 10, 2024

    • ggrossha-ProteaseSpecificity-qPISA

      Public
      Code to accompany our paper "Massively parallel quantification of substrate turnoverdefines protease subsite cooperativity"
      R
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024