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    24 repositories

    • heldring-E2S-modeling

      Public
      Data and code used for the manuscript titled "Interdependency of estradiol-mediated ERα activation and subsequent PR and GREB1 induction to control cell cycle progression"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 14, 2024Sep 14, 2024

    • FunGen2024

      Public
      Code to test if DESeq2 can be run for the bachelor course Functional Genomics
      0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • Leegwater_lipidomics_normalization

      Public
      Code and example dataset to generate figures for "Normalization strategies for lipidome data in cell line panels" (Leegwater et al. submitted)
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 19, 2024Mar 19, 2024

    • Sharma_Nitrofurantoin_PBPKmodeling

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • beltman-DRAGbarcode-cleanup

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • lems-emt-pdl1-models-figures

      Public
      Model plus code to generate figures for Lems et al. 2023. Tumor-Mediated Immunosuppression and Cytokine Spreading Affects the Relation Between EMT and PD-L1 Status. doi: 10.3389/fimmu.2023.1219669
      Component Pascal
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Jul 4, 2023Jul 4, 2023

    • LAG_TIM_BIOMARKERS

      Public
      R
      •0•0•0•0•Updated Mar 28, 2023Mar 28, 2023

    • H5CellProfiler

      Public
      H5CellProfiler: User-friendly high-content CellProfiler imaging data analysis in R
      R
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2023Feb 13, 2023

    • burger-emt-pdl1-models-figures

      Public
      Models and code to generate figures for Burger et al. 2022. Bidirectional Crosstalk Between Epithelial-Mesenchymal Plasticity and IFNγ-Induced PD-L1 Expression Promotes Tumor Progression. bioRxiv. https://doi.org/10.1101/2022.02.03.478950
      Component Pascal
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Aug 30, 2022Aug 30, 2022

    • heldring-spatial-liver-model

      Public
      Models, code and data to reproduce the results from the spatial liver model manuscript.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 8, 2022Jul 8, 2022

    • heldring_phh_code

      Public
      Models and code to reproduce data analysis, simulations, parameter optimization and to generate figures.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 23, 2022May 23, 2022

    • mito-mor-classification

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2022Mar 24, 2022

    • bartSeq

      Public
      Software required for Bart-Seq technology – a cheap technology to analyze (single) cells using forward and reverse barcoding for target genes
      Python
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Dec 16, 2021Dec 16, 2021

    • morpheus-pseudopodia

      Public
      Morpheus plugin for adding pseudopod-driven persistence
      C++
      •
      Other
      •0•0•0•0•Updated Sep 7, 2021Sep 7, 2021

    • Frontiers_pharmacology_MitoMMP

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 8, 2021Aug 8, 2021

    • CTL_killing_insufficient

      Public
      C++
      •0•0•0•0•Updated May 20, 2021May 20, 2021

    • CD137_Tcells_ODE

      Public
      HTML
      •0•0•0•0•Updated May 20, 2021May 20, 2021

    • Tcellactivation_ODE_Immunity2020

      Public
      Code needed for the modeling and fitting in Zenke et al, Immunity, 2020
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Nov 8, 2020Nov 8, 2020

    • python-course-materials

      Public
      Jupyter Notebook
      •6•0•0•0•Updated Oct 14, 2019Oct 14, 2019

    • basic-programming-in-drug-discovery

      Public
      Course materials for basic programming in drug discovery
      Jupyter Notebook
      •3•4•0•0•Updated Feb 8, 2019Feb 8, 2019

    • wmc_imagej

      Public
      Macro to use WMC segment in batch mode in Fiji
      0•0•0•0•Updated May 18, 2018May 18, 2018

    • cellprofiler-plugins

      Public
      0•1•0•0•Updated Feb 2, 2018Feb 2, 2018

    • ClonalGrowthSimulator_ABM

      Public
      Agent based simulator of clonal growth
      C++
      •
      MIT License
      •0•0•0•0•Updated Jan 18, 2018Jan 18, 2018

    • ClonalGrowthSimulator_SSA

      Public
      Gillespie simulator of clonal growth
      C++
      •
      MIT License
      •1•0•0•0•Updated Jan 18, 2018Jan 18, 2018