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@PMBio Probabilistic Models in Biology

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    52 repositories

    • deeprvat

      Public
      Python
      •
      Other
      •6•35•2•2•Updated Dec 23, 2024Dec 23, 2024

    • SpatialDE

      Public
      Test genes for Spatial Variation
      Python
      •
      MIT License
      •57•13•0•0•Updated Dec 20, 2024Dec 20, 2024

    • pypi-download-stats

      Public
      Notebooks to plot download stats for PyPI packages
      Jupyter Notebook
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • spatialdata-workshops

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•12•5•1•Updated Dec 10, 2024Dec 10, 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 CHROMOTHRIPTIC MEDULLOBLASTOMA HIGHLIGHTS GENOMIC AND TRANSCRIPTOMIC CONSEQUENCES OF GENOME INSTABILITY".
      Jupyter Notebook
      •2•4•0•0•Updated Oct 11, 2024Oct 11, 2024

    • spaceTree

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

    • deeprvat-analysis

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

    • bicycle

      Public
      Bicycle: Intervention-Based Causal Discovery with Cycles
      Jupyter Notebook
      •3•30•1•1•Updated Jul 17, 2024Jul 17, 2024

    • MetH5Format

      Public
      HDF5-based container format for Methylation calls from long reads
      Python
      •
      MIT License
      •2•7•3•0•Updated Jan 24, 2024Jan 24, 2024

    • MuDataSeurat

      Public
      .h5mu files interface for Seurat
      scrna-seqmulti-omicsseuratanndatamudatamultimodal-omics
      R
      •11•27•5•1•Updated Nov 28, 2023Nov 28, 2023

    • ase_spermatogenesis

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

    • MultiOmicsCourse

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•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 signature"
      Python
      •
      GNU General Public License v3.0
      •0•6•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•28•2•0•Updated Jul 3, 2023Jul 3, 2023

    • SingleCellCourse

      Public
      Jupyter Notebook
      •10•5•0•0•Updated May 31, 2023May 31, 2023

    • bonito

      Public
      A PyTorch Basecaller for Oxford Nanopore Reads
      Python
      •
      Other
      •122•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•2•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 the correction of confounding sources of variation.
      HTML
      •
      Apache License 2.0
      •46•104•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
      •21•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•0•0•0•Updated Sep 21, 2021Sep 21, 2021

    • hipsci_pipeline

      Public
      Python
      •1•1•10•0•Updated Mar 30, 2021Mar 30, 2021

    • hca_organoid_pipelines

      Public
      Pipelines for HCA|Organoid data processing
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•0•0•0•Updated Feb 28, 2021Feb 28, 2021

    • scmt_splicing

      Public
      Jupyter Notebook
      •
      Other
      •1•4•1•0•Updated Jan 17, 2019Jan 17, 2019

    • scMT-seq

      Public
      HTML
      •5•14•0•1•Updated Nov 9, 2018Nov 9, 2018

    • stepwise-elnet

      Public
      Code to perform step wise elastic net analysis
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jul 3, 2018Jul 3, 2018