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Showing content from https://github.com/saeyslab below:

Saeys Lab · GitHub

Data Mining and Modelling for Biomedicine, a VIB-UGent research unit

1. NicheNet: predict active ligand-target links between interacting cells

   R 559 128

2. Using self-organizing maps for visualization and interpretation of cytometry data

   R 29 8

3. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

   HTML 151 19

4. Peak-based selection of high quality cytometry data

   R 17 9

5. A repository for benchmarking spatial deconvolution and mapping tools

   R 34 4

6. R library to normalize cytometry data

   R 37 11

• multinichenetr Public

  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

  saeyslab/multinichenetr’s past year of commit activity HTML 151 GPL-3.0 19 11 1 Updated Aug 12, 2025
• saeyslab/gradient-regularisation-interpretability’s past year of commit activity Python 0 0 0 0 Updated Aug 11, 2025
• harpy Public

  Single-cell spatial proteomics analysis that makes you happy!

  saeyslab/harpy’s past year of commit activity Python 35 6 14 1 Updated Aug 11, 2025
• FlowSOM_Python Public

  The complete FlowSOM package known from R, now available in Python!

  saeyslab/FlowSOM_Python’s past year of commit activity Python 22 GPL-3.0 5 2 1 Updated Aug 11, 2025
• ViVAE Public

  Single-cell dimensionality reduction toolkit

  saeyslab/ViVAE’s past year of commit activity Jupyter Notebook 8 Apache-2.0 1 0 0 Updated Aug 11, 2025
• ViScore Public

  Single-cell dimensionality reduction evaluation and benchmarking toolkit

  saeyslab/ViScore’s past year of commit activity Python 7 Apache-2.0 0 1 0 Updated Aug 11, 2025
• SingleBench Public

  Evaluation framework for exploratory modelling in cytometry

  saeyslab/SingleBench’s past year of commit activity R 0 MIT 0 1 0 Updated Aug 7, 2025
• iidx Public

  Interactive and interpretable differential expression modelling in cytometry

  saeyslab/iidx’s past year of commit activity R 0 Apache-2.0 0 0 0 Updated Aug 6, 2025
• FlowSOM Public

  Using self-organizing maps for visualization and interpretation of cytometry data

  saeyslab/FlowSOM’s past year of commit activity R 29 8 5 0 Updated Aug 1, 2025
• saeyslab/napari-sparrow’s past year of commit activity Python 29 0 13 0 Updated Jul 31, 2025

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