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@PMBio Probabilistic Models in Biology

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    57 repositories

    • LIVI

      Public
      LIVI is an interpretable deep learning framework that enables trans-eQTL mapping at single-cell resolution.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•0•0•Updated Feb 10, 2026Feb 10, 2026

    • Health-Privacy-Challenge

      Public
      The starter kit for the CAMDA 2026 Health Privacy Challenge.
      privacyrna-seqscrna-seqsingle-cellgenerative-modelsmembership-inference-attacksynthetic-data-generationtrustworthy-ai
      Python
      •
      GNU General Public License v3.0
      •7•6•0•1•Updated Jan 21, 2026Jan 21, 2026

    • interp-extrap-perturb

      Public
      https://interp-extrap-perturb.readthedocs.io
      Jinja
      •
      MIT License
      •2•6•4•1•Updated Jan 13, 2026Jan 13, 2026

    • spatialdata-workshops

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•13•5•1•Updated Dec 20, 2025Dec 20, 2025

    • polygenic_germline_risk

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 24, 2025Sep 24, 2025

    • GBM_analysis

      Public
      Notebooks and scripts used to analyse GBM multi-ome atlas
      Jupyter Notebook
      •2•3•0•0•Updated Aug 27, 2025Aug 27, 2025

    • deeprvat

      Public
      Python
      •
      Other
      •8•41•3•2•Updated Jun 16, 2025Jun 16, 2025

    • bicycle

      Public
      Bicycle: Intervention-Based Causal Discovery with Cycles
      Jupyter Notebook
      •7•36•1•0•Updated Jun 3, 2025Jun 3, 2025

    • scDoRI

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 14, 2025Apr 14, 2025

    • SpatialDE

      Public
      Test genes for Spatial Variation
      Python
      •
      MIT License
      •59•15•0•0•Updated Dec 20, 2024Dec 20, 2024

    • MB_scSeq

      Public
      This repo contains scripts for the analysis of scDNA- and scSeq data from LFS medulloblastoma accompanying the manuscript "SINGLE CELL MULTI-OMICS ANALYSIS OF C…
      Jupyter Notebook
      •2•4•0•0•Updated Oct 11, 2024Oct 11, 2024

    • spaceTree

      Public
      Jupyter Notebook
      •
      MIT License
      •1•7•1•0•Updated Sep 16, 2024Sep 16, 2024

    • deeprvat-analysis

      Public
      Python
      •0•3•1•0•Updated Jul 18, 2024Jul 18, 2024

    • MetH5Format

      Public
      HDF5-based container format for Methylation calls from long reads
      Python
      •
      MIT License
      •1•7•4•0•Updated Jan 24, 2024Jan 24, 2024

    • MuDataSeurat

      Public
      .h5mu files interface for Seurat
      scrna-seqmulti-omicsseuratanndatamudatamultimodal-omics
      R
      •14•32•7•1•Updated Nov 28, 2023Nov 28, 2023

    • ase_spermatogenesis

      Public
      HTML
      •1•1•0•0•Updated Nov 17, 2023Nov 17, 2023

    • MultiOmicsCourse

      Public
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Nov 10, 2023Nov 10, 2023

    • spava

      Public
      Python
      •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • mb-nanopore-2022

      Public
      Analysis code for publication "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatur…
      Python
      •
      GNU General Public License v3.0
      •0•7•1•0•Updated Sep 18, 2023Sep 18, 2023

    • pycoMeth

      Public
      DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
      Python
      •
      GNU General Public License v3.0
      •3•30•3•0•Updated Jul 3, 2023Jul 3, 2023

    • SingleCellCourse

      Public
      Jupyter Notebook
      •9•4•0•0•Updated May 31, 2023May 31, 2023

    • bonito

      Public
      A PyTorch Basecaller for Oxford Nanopore Reads
      Python
      •
      Other
      •134•0•0•0•Updated Jan 16, 2023Jan 16, 2023

    • mudatasets

      Public
      Multimodal datasets, in MuData format
      muonscrna-seqmulti-omicsscanpyanndatamudatamultiomemultimodal-omics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•2•0•Updated Jan 13, 2023Jan 13, 2023

    • scLVM

      Public
      scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for …
      HTML
      •
      Apache License 2.0
      •46•110•16•2•Updated Dec 16, 2022Dec 16, 2022

    • spatial-club-heidelberg

      Public
      For scripts for downloading and processing data from different spatial technologies
      0•0•0•0•Updated Oct 7, 2022Oct 7, 2022

    • remora

      Public
      Methylation/modified base calling separated from basecalling.
      Python
      •
      Other
      •26•0•0•0•Updated Jun 24, 2022Jun 24, 2022

    • scdali

      Public
      scDALI: Modelling allelic imbalance in single cells.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•1•0•Updated Jun 23, 2022Jun 23, 2022

    • scdali_analyses

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 18, 2021Nov 18, 2021

    • muon.r

      Public
      R ⇄ .h5mu I/O for multimodal data
      R
      •0•1•0•0•Updated Oct 12, 2021Oct 12, 2021

    • spatialde2-paper

      Public
      Code to reproduce the figures (data not included)
      Jupyter Notebook
      •0•1•0•0•Updated Sep 21, 2021Sep 21, 2021