All

70 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
•7•60•20•3•Updated Apr 23, 2026Apr 23, 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•28•3•5•Updated Apr 20, 2026Apr 20, 2026
iidx
Public
Interactive and interpretable differential expression modelling in cytometry
R
•
Apache License 2.0
•0•0•0•0•Updated Apr 17, 2026Apr 17, 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
FlowSOM
Public
Using self-organizing maps for visualization and interpretation of cytometry data
R
•8•35•6•0•Updated Apr 10, 2026Apr 10, 2026
PeacoQC
Public
Peak-based selection of high quality cytometry data
R
•11•21•3•0•Updated Feb 23, 2026Feb 23, 2026
harpy_figures
Public
Jupyter Notebook
•0•1•0•0•Updated Feb 11, 2026Feb 11, 2026
napari-sparrow
Public
https://sparrow-pipeline.readthedocs.io/en/latest/
Python
•
Other
•0•33•13•3•Updated Feb 6, 2026Feb 6, 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
CytoNorm
Public
R library to normalize cytometry data
R
•11•39•32•0•Updated Jan 16, 2026Jan 16, 2026
PIDgeon
Public
PIDgeon: pipeline for processing cytometry data after PID screening with generation of patient reports
Jupyter Notebook
•0•2•0•0•Updated Jan 8, 2026Jan 8, 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
•136•639•28•0•Updated Nov 12, 2025Nov 12, 2025
ExtractInfinicyt
Public
Script to extract fcs files and gating information from infinicyt .CYT files
Java
•0•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
•4•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
•
GNU General Public License v3.0
•20•185•17•1•Updated Aug 12, 2025Aug 12, 2025
gradient-regularisation-interpretability
Public
Python
•0•0•0•0•Updated Aug 11, 2025Aug 11, 2025
ViVAE
Public
Single-cell dimensionality reduction toolkit
deep-learning dimensionality-reduction scrna-seq
deep-learning dimensionality-reduction scrna-seq differential-geometry mds cytometry single-cell-analysis
Jupyter Notebook
•
Apache License 2.0
•2•11•0•0•Updated Aug 11, 2025Aug 11, 2025
ViScore
Public
Single-cell dimensionality reduction evaluation and benchmarking toolkit
benchmarking dimensionality-reduction scrna-seq
benchmarking dimensionality-reduction scrna-seq cytometry single-cell-analysis
Python
•
Apache License 2.0
•1•10•1•0•Updated Aug 11, 2025Aug 11, 2025
SingleBench
Public
Evaluation framework for exploratory modelling in cytometry
R
•
MIT License
•0•0•1•0•Updated Aug 7, 2025Aug 7, 2025
polygloty
Public
HTML
•
MIT License
•0•3•0•1•Updated Jul 29, 2025Jul 29, 2025
spotless-benchmark
Public
A repository for benchmarking spatial deconvolution and mapping tools
R
•
MIT License
•5•36•0•0•Updated May 13, 2025May 13, 2025
hydra_hpc_example
Public
Hydra HPC example
python hpc slurm
python hpc slurm hydra
Python
•0•7•0•0•Updated Dec 9, 2024Dec 9, 2024
CytoBright
Public
Estimate Stain Index for single stained cytometry files.
R
•
GNU General Public License v3.0
•1•7•0•1•Updated Sep 27, 2024Sep 27, 2024
nichenet_training
Public
R
•0•1•0•0•Updated Sep 10, 2024Sep 10, 2024
VIB_Hackathon_June_2024
Public
Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8T
Jupyter Notebook
•
MIT License
•4•2•2•0•Updated Jun 24, 2024Jun 24, 2024

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Saeys Lab

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All

70 repositories

harpy

FlowSOM_Python

iidx

DSFCM_meeting2026

nichenet_protocol

marble-sorter-ui

FlowSOM

PeacoQC

harpy_figures

napari-sparrow

adversarial-mri

ComputationalCytometry

CytoNorm

PIDgeon

nichenetr

ExtractInfinicyt

TENET

CeSpGRN

FAIR2025_Tutorial_TRACE

multinichenetr

gradient-regularisation-interpretability

ViVAE

ViScore

SingleBench

polygloty

spotless-benchmark

hydra_hpc_example

CytoBright

nichenet_training

VIB_Hackathon_June_2024

All

All

Repositories list

70 repositories