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@Moldia

Molecular Diagnostics (Mats Nilsson research group)

Scripts and softwares used in research

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  1. Xenium_benchmarking Xenium_benchmarking Public

    Code used to benchmark Xenium

    Jupyter Notebook 37 5

  2. multi_padlock_design multi_padlock_design Public

    Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

    Python 12 13

  3. Lee_2023 Lee_2023 Public

    All the code described in the Lee et al. (2023) paper

    Jupyter Notebook 6 4

  4. in_situ_seq in_situ_seq Public

    Basic analysis pipeline for in situ sequencing

    MATLAB 5 2

  5. Tools Tools Public

    Repository containing all the preprocessing and analysis tools generated in Molecular Diagnosis group, Science for Life Laboratories, Stockholm University, Sweden

    MATLAB 4 3

  6. heart heart Public

    scripts and viewer used for "A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart"

    JavaScript 2

Repositories

Showing 10 of 30 repositories
  • Lee_2023 Public

    All the code described in the Lee et al. (2023) paper

    Moldia/Lee_2023’s past year of commit activity
    Jupyter Notebook 6 4 6 0 Updated Sep 17, 2024
  • multi_padlock_design Public

    Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

    Moldia/multi_padlock_design’s past year of commit activity
    Python 12 MIT 13 7 0 Updated Jul 11, 2024
  • Xenium_benchmarking Public

    Code used to benchmark Xenium

    Moldia/Xenium_benchmarking’s past year of commit activity
    Jupyter Notebook 37 5 4 0 Updated Jun 30, 2024
  • GBmap_ISS Public

    Code used in the publication "Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma" for the analysis of ISS data

    Moldia/GBmap_ISS’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Apr 22, 2024
  • PLP_directRNA_design Public

    Package used to create padlock probes that target RNA directly. It can be used for any gene and species.

    Moldia/PLP_directRNA_design’s past year of commit activity
    Python 0 MIT 1 1 0 Updated Jan 31, 2024
  • cellular-architecture-of-evolving-neuroinflammatory-lesions-and-multiple-sclerosis-pathology Public
    Moldia/cellular-architecture-of-evolving-neuroinflammatory-lesions-and-multiple-sclerosis-pathology’s past year of commit activity
    Jupyter Notebook 2 0 0 0 Updated Jan 29, 2024
  • ISS_postprocessing Public
    Moldia/ISS_postprocessing’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Sep 25, 2023
  • ISS_decoding Public
    Moldia/ISS_decoding’s past year of commit activity
    Jupyter Notebook 1 0 1 1 Updated Sep 25, 2023
  • ISS_CARE Public
    Moldia/ISS_CARE’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 25, 2023
  • ISS_deconvolution Public

    Repository to do image deconvolution on ISS datasets using Flowdec

    Moldia/ISS_deconvolution’s past year of commit activity
    Jupyter Notebook 0 0 1 0 Updated Sep 25, 2023
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