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    38 repositories

    • Delphi

      Public
      Jupyter Notebook
      •
      MIT License
      •3•16•0•0•Updated Dec 24, 2024Dec 24, 2024

    • Hetairos

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

    • segger

      Public
      a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).
      Python
      •
      MIT License
      •3•1•0•0•Updated Oct 16, 2024Oct 16, 2024

    • CHOCOLAT-G2P

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jul 4, 2024Jul 4, 2024

    • CancerRisk

      Public
      HTML
      •
      MIT License
      •1•6•0•0•Updated Jul 3, 2024Jul 3, 2024

    • SARS-CoV-2-International

      Public
      International SARS-CoV-2 surveillance
      Jupyter Notebook
      •6•36•3•1•Updated May 19, 2023May 19, 2023

    • genomicsurveillance

      Public
      Jupyter Notebook
      •
      MIT License
      •7•7•0•0•Updated Jan 2, 2023Jan 2, 2023

    • SARS-CoV-2-Germany

      Public
      SARS-CoV-2 genomic surveillance in Germany
      Jupyter Notebook
      •
      The Unlicense
      •0•1•0•0•Updated Dec 6, 2022Dec 6, 2022

    • BaSISS

      Public
      Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
      cancer-genomicsspatial-transcriptomics
      Jupyter Notebook
      •
      MIT License
      •2•24•0•0•Updated Nov 21, 2022Nov 21, 2022

    • uk_biobank_survival

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 6, 2022Sep 6, 2022

    • ProbCox

      Public
      Probabilistic Cox Regression
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Sep 1, 2022Sep 1, 2022

    • ebmstate_paper_data_files

      Public
      HTML
      •0•1•0•0•Updated Jun 22, 2022Jun 22, 2022

    • deepSNV

      Public
      The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.
      R
      •6•14•1•0•Updated Jun 1, 2022Jun 1, 2022

    • clonal_dynamics

      Public
      Code repository for the longitudinal and phylodynamic analysis in "The longitudinal dynamics and natural history of clonal haematopoiesis"
      R
      •1•0•0•0•Updated Mar 21, 2022Mar 21, 2022

    • scHierarchy

      Public
      A toolking for cell type hierarchies: marker selection & consistent classification
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Feb 22, 2022Feb 22, 2022

    • wbs-prediction

      Public
      Code repository for a project focused on diagnostic prediction from whole blood slides
      Jupyter Notebook
      •1•0•0•0•Updated Feb 11, 2022Feb 11, 2022

    • omero_setup

      Public
      0•0•0•0•Updated Feb 8, 2022Feb 8, 2022

    • ebmstate

      Public
      An R package for Empirical Bayes MultiState models
      R
      •1•1•0•0•Updated Feb 4, 2022Feb 4, 2022

    • postcode

      Public
      Decoding of image-based spatial transcriptomics
      Jupyter Notebook
      •
      MIT License
      •6•3•0•0•Updated Oct 26, 2021Oct 26, 2021

    • gerstung-lab.github.io

      Public
      HTML
      •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

    • radiation

      Public
      Codes for the analysis of C. elegant samples of different DNA repair deficient backgrounds exposed to ionising radiation.
      R
      •1•0•0•0•Updated Aug 31, 2021Aug 31, 2021

    • BarrettsProgressionRisk

      Public
      An R package to process and predict risk of adenocarcinoma progression from shallow whole-genome sequencing data.
      R
      •6•5•0•0•Updated Jun 22, 2021Jun 22, 2021

    • sarscov2-b117

      Public
      Spatiotemporal analysis of strain-specific B.1.1.7 SARS-CoV-2 infection dynamics
      Jupyter Notebook
      •1•8•0•0•Updated Dec 30, 2020Dec 30, 2020

    • signature-interactions

      Public
      Mutational signatures are jointly shaped by DNA damage and repair
      HTML
      •3•6•0•0•Updated Dec 17, 2020Dec 17, 2020

    • PC-CHiP

      Public
      Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis
      Python
      •28•75•0•0•Updated Dec 17, 2020Dec 17, 2020

    • MutationTimeR

      Public
      An R package to time somatic mutations
      R
      •24•60•10•0•Updated Dec 12, 2020Dec 12, 2020

    • mutationaccumulation

      Public
      Codes for a publication about mutation accumulation in >60 DNA repair deficient C. elegant lines (Meier et al, under preparation).
      R
      •2•1•0•0•Updated Nov 22, 2020Nov 22, 2020

    • tensorsignatures

      Public
      A python package for learning mutational signatures and their multidimensional genomic properties
      Jupyter Notebook
      •
      MIT License
      •4•14•0•0•Updated Sep 1, 2020Sep 1, 2020

    • ebsurv

      Public
      R
      •0•1•0•0•Updated Jul 28, 2020Jul 28, 2020

    • CoxHD

      Public
      An R package containing high-dimensional extensions of the Cox model
      HTML
      •12•7•0•0•Updated Jul 17, 2020Jul 17, 2020