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79 repositories

harpy
Public
Single-cell spatial omics analysis that makes you happy!
machine-learning bioinformatics hpc
machine-learning bioinformatics hpc spatial microscopy analysis-framework spatialdata spatial-omics
Python
•
Other
•8•70•28•2•Updated Aug 8, 2026Aug 8, 2026
SaeysLab-Github-stats
Public
An inventory and summary of all public repositories of the Saeys Lab organization
github-api streamlit
github-api streamlit
Python
•0•0•0•0•Updated Aug 6, 2026Aug 6, 2026
nichenetpy
Public
rna-seq gene-expression network-inference
rna-seq gene-expression network-inference data-integration single-cell-rna-seq single-cell-omics intercellular-communication ligand-receptor ligand-target cell-cell-communication
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•14•4•0•Updated Aug 4, 2026Aug 4, 2026
FlowSOM_Python
Public
The complete FlowSOM package known from R, now available in Python!
machine-learning bioinformatics clustering
machine-learning bioinformatics clustering flowcytometry
Python
•
GNU General Public License v3.0
•7•34•3•5•Updated Aug 3, 2026Aug 3, 2026
napari-sparrow
Public
https://sparrow-pipeline.readthedocs.io/en/latest/
Python
•
Other
•0•34•13•1•Updated Jul 31, 2026Jul 31, 2026
sparrow-notebooks
Public
Repo to store the large tutorial notebooks of the SPArrOW package
0•0•2•0•Updated Jul 31, 2026Jul 31, 2026
pddshap
Public
Python
•1•1•0•0•Updated Jul 29, 2026Jul 29, 2026
FlowSOM
Public
Using self-organizing maps for visualization and interpretation of cytometry data
R
•9•36•6•0•Updated Jul 23, 2026Jul 23, 2026
CytoNorm
Public
R library to normalize cytometry data
R
•12•41•33•0•Updated Jul 7, 2026Jul 7, 2026
iidx
Public
Interactive and interpretable differential expression modelling in cytometry
R
•
Apache License 2.0
•0•0•0•0•Updated Jun 11, 2026Jun 11, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•84•0•0•0•Updated Jun 2, 2026Jun 2, 2026
nichenetr
Public
NicheNet: predict active ligand-target links between interacting cells
rna-seq gene-expression network-inference
rna-seq gene-expression network-inference data-integration single-cell-rna-seq single-cell-omics intercellular-communication ligand-receptor ligand-target cell-cell-communication
R
•134•670•26•0•Updated Jun 1, 2026Jun 1, 2026
MedialAxisMapping
Public
Global alignment of CLEM images based on blood vessel patterns
Jupyter Notebook
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MIT License
•0•0•0•0•Updated May 28, 2026May 28, 2026
BonteEtAl_AML_Dx_EuroFlow
Public
Code for the paper Bonte S et al. Old data, new tricks: Comprehensive computational analysis of 10 years of multi-center EuroFlow acute myeloid leukemia diagnos…
R
•0•0•0•0•Updated Apr 29, 2026Apr 29, 2026
OrgaCCC
Public
Python
•1•0•0•0•Updated Apr 28, 2026Apr 28, 2026
GCNLA
Public
Python
•1•0•0•0•Updated Apr 27, 2026Apr 27, 2026
DSFCM_meeting2026
Public
Scripts that were used to analyze the shared dataset during the “One Dataset, Many Perspectives: Flow Cytometry Analysis Workflows” DSFCM meeting
0•0•0•0•Updated Apr 16, 2026Apr 16, 2026
nichenet_protocol
Public
HTML
•
MIT License
•1•4•1•0•Updated Apr 15, 2026Apr 15, 2026
marble-sorter-ui
Public
Interface for the marble sorter
Python
•
MIT License
•0•0•0•0•Updated Apr 15, 2026Apr 15, 2026
PeacoQC
Public
Peak-based selection of high quality cytometry data
R
•12•22•3•0•Updated Feb 23, 2026Feb 23, 2026
harpy_figures
Public
Jupyter Notebook
•0•1•0•0•Updated Feb 11, 2026Feb 11, 2026
adversarial-mri
Public
Triggering hallucinations in model-based MRI reconstruction via adversarial perturbations
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Jan 23, 2026Jan 23, 2026
ComputationalCytometry
Public
Workshop computational cytometry
R
•1•3•0•0•Updated Jan 19, 2026Jan 19, 2026
PIDgeon
Public
PIDgeon: pipeline for processing cytometry data after PID screening with generation of patient reports
Jupyter Notebook
•0•3•0•0•Updated Jan 8, 2026Jan 8, 2026
ExtractInfinicyt
Public
Script to extract fcs files and gating information from infinicyt .CYT files
Java
•1•2•0•0•Updated Oct 29, 2025Oct 29, 2025
TENET
Public
Python
•1•0•0•0•Updated Oct 22, 2025Oct 22, 2025
CeSpGRN
Public
CeSpGRN: Inferring cell specific GRN using single-cell gene expression data
Python
•
GNU General Public License v3.0
•5•0•0•0•Updated Oct 21, 2025Oct 21, 2025
FAIR2025_Tutorial_TRACE
Public
Data exploration and visualisation of cytometry data with TRACE
Python
•0•0•0•0•Updated Oct 13, 2025Oct 13, 2025
multinichenetr
Public
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
systems-biology scrna-seq single-cell
systems-biology scrna-seq single-cell differential-expression single-cell-rna-seq intercellular-communication ligand-receptor ligand-target cell-cell-interaction cell-cell-communication
HTML
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GNU General Public License v3.0
•21•195•20•1•Updated Aug 12, 2025Aug 12, 2025
gradient-regularisation-interpretability
Public
Python
•0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

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79 repositories