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@fmi-basel Friedrich Miescher Institute for Biomedical Research

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    74 repositories

    • faim-jetraw

      Public
      Python
      •
      Apache License 2.0
      •0•0•3•1•Updated Oct 14, 2024Oct 14, 2024

    • gfriedri_dataset-alignment

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

    • gpeters-fetchNOMe

      Public
      R package for fetching NOMe-seq data from BAM files
      C++
      •
      Other
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • faim-robocopy

      Public
      A python-based UI for robocopy
      Python
      •
      MIT License
      •0•3•7•1•Updated Oct 7, 2024Oct 7, 2024

    • gfriedri-em-alignment-flows

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

    • stork

      Public
      A differentiable spiking neural network simulator
      Python
      •
      MIT License
      •4•14•0•0•Updated Sep 25, 2024Sep 25, 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

    • neural-decoding-RSNN

      Public
      Recurrent spiking neural networks (RSNNs) for decoding of motor signals from cortical spike trains
      Python
      •
      MIT License
      •0•3•0•0•Updated Sep 2, 2024Sep 2, 2024

    • gliberal-scMultipleX

      Public
      Feature extraction and linking of multiplexing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•8•18•1•Updated Aug 24, 2024Aug 24, 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

    • GUIFold

      Public
      GUI for running jobs with a local installation of AlphaFold2. Supports submission to queuing systems.
      guipipelinealphafold2alphafold-multimer
      Python
      •
      Apache License 2.0
      •0•6•0•0•Updated Aug 7, 2024Aug 7, 2024

    • guifold-alphafold2

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •2.2k•1•0•0•Updated Aug 7, 2024Aug 7, 2024

    • binary-activation-maps-sqp

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 5, 2024Jul 5, 2024

    • splitrsync

      Public
      A tool to parallelize rsync based transfers
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 28, 2024Jun 28, 2024

    • improc

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 30, 2024May 30, 2024

    • faim-retina-chatbands

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 27, 2024May 27, 2024

    • surrogate-gradient-theory

      Public
      Jupyter Notebook
      •0•3•0•0•Updated May 3, 2024May 3, 2024

    • 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 May 3, 2024May 3, 2024

    • faim-ij1-io

      Public
      A simple IJ2 wrapper for reading and writing TIFF files through IJ1
      Java
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated May 2, 2024May 2, 2024

    • faim-ij2-ij

      Public
      Simple headless SciJava wrappers around ImageJ plugins
      Java
      •
      MIT License
      •0•0•0•0•Updated May 2, 2024May 2, 2024

    • gbuehler-MiniChip

      Public
      small collection of R functions for ChIPseq analysis
      HTML
      •1•2•0•0•Updated Apr 22, 2024Apr 22, 2024

    • neuRoi

      Public
      MATLAB
      •5•1•7•0•Updated Apr 12, 2024Apr 12, 2024

    • gchao-koopa-flows

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 9, 2024Feb 9, 2024

    • dl-utils

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • gbuehler-dinoR

      Public
      R package for differential NOMe-seq data analysis.
      R
      •0•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • latent-predictive-learning

      Public
      Code to accompany our paper "The combination of Hebbian and predictive plasticity learns invariant object representations in deep sensory networks” bioRxiv 2022
      deep-learningself-supervised-learninghebbian-plasticity
      Jupyter Notebook
      •
      MIT License
      •5•22•0•0•Updated Jan 16, 2024Jan 16, 2024

    • ggiorget-spt-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • gchao_RPL-Myc

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 11, 2023Dec 11, 2023

    • gliberal-lightsheet-2023

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 28, 2023Nov 28, 2023

    • HT_OrganoidAnalysis

      Public
      Code accompanying the manuscript "Dynamics and plasticity of stem cells in the regenerating human colonic epithelium" by Oost, Kahnwald et al. from the Liberali Lab.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 19, 2023Nov 19, 2023