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61 repositories

harpy
Public
Single-cell spatial proteomics analysis that makes you happy!
machine-learning bioinformatics hpc spatial microscopy analysis-framework napari-plugin
Python
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Other
•5•28•12•2•Updated May 23, 2025May 23, 2025
nichenetr
Public
NicheNet: predict active ligand-target links between interacting cells
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
•125•538•22•2•Updated May 23, 2025May 23, 2025
ViVAE
Public
Single-cell dimensionality reduction toolkit
deep-learning dimensionality-reduction scrna-seq differential-geometry mds cytometry single-cell-analysis
Jupyter Notebook
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Apache License 2.0
•1•6•0•0•Updated May 21, 2025May 21, 2025
FlowSOM_Python
Public
The complete FlowSOM package known from R, now available in Python!
machine-learning bioinformatics clustering flowcytometry
Python
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GNU General Public License v3.0
•5•20•2•1•Updated May 19, 2025May 19, 2025
SingleBench
Public
Evaluation framework for exploratory modelling in cytometry
R
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MIT License
•0•0•0•0•Updated May 16, 2025May 16, 2025
PeacoQC
Public
Peak-based selection of high quality cytometry data
R
•9•16•3•0•Updated May 13, 2025May 13, 2025
spotless-benchmark
Public
A repository for benchmarking spatial deconvolution and mapping tools
R
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MIT License
•4•33•0•0•Updated May 13, 2025May 13, 2025
ViScore
Public
Single-cell dimensionality reduction evaluation and benchmarking toolkit
benchmarking dimensionality-reduction scrna-seq cytometry single-cell-analysis
Python
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Apache License 2.0
•0•6•1•0•Updated May 6, 2025May 6, 2025
napari-sparrow
Public
https://sparrow-pipeline.readthedocs.io/en/latest/
Python
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Other
•0•27•13•0•Updated May 6, 2025May 6, 2025
iidx
Public
Interactive and interpretable differential expression modelling in cytometry
R
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Apache License 2.0
•0•0•0•0•Updated Apr 26, 2025Apr 26, 2025
ComputationalCytometry
Public
Workshop computational cytometry
R
•0•2•0•0•Updated Apr 15, 2025Apr 15, 2025
nichenet_protocol
Public
HTML
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MIT License
•0•0•0•0•Updated Apr 2, 2025Apr 2, 2025
CytoNorm
Public
R library to normalize cytometry data
R
•11•36•32•0•Updated Apr 1, 2025Apr 1, 2025
FlowSOMPublic
Using self-organizing maps for visualization and interpretation of cytometry data
R
•8•27•5•0•Updated Mar 17, 2025Mar 17, 2025
marble-sorter-ui
Public
Interface for the marble sorter
Python
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MIT License
•0•0•0•0•Updated Mar 7, 2025Mar 7, 2025
gradient-regularisation-interpretability
Public
Python
•0•0•0•0•Updated Feb 26, 2025Feb 26, 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 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
•17•146•10•0•Updated Jan 14, 2025Jan 14, 2025
hydra_hpc_example
Public
Hydra HPC example
python hpc slurm hydra
Python
•0•5•0•0•Updated Dec 9, 2024Dec 9, 2024
CytoBright
Public
Estimate Stain Index for single stained cytometry files.
R
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GNU General Public License v3.0
•1•4•0•0•Updated Sep 27, 2024Sep 27, 2024
polygloty
Public
HTML
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MIT License
•0•2•0•1•Updated Sep 24, 2024Sep 24, 2024
nichenet_training
Public
R
•1•1•0•0•Updated Sep 10, 2024Sep 10, 2024
ExtractInfinicyt
Public
Script to extract fcs files and gating information from infinicyt .CYT files
Java
•0•0•0•0•Updated Jul 16, 2024Jul 16, 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
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MIT License
•4•2•2•0•Updated Jun 24, 2024Jun 24, 2024
spatial_ccc_experiments
Public
Jupyter Notebook
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MIT License
•1•1•7•3•Updated Jun 13, 2024Jun 13, 2024
synthspot
Public
synthspot: package to generate synthetic Visium-like spot data
R
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GNU General Public License v3.0
•3•5•0•0•Updated May 16, 2024May 16, 2024
cifconvert
Public
cifconvert is a package built on the python-bioformats package that saves images and masks from the proprietary Amnis CIF-file format to an HDF5 file.
Python
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GNU General Public License v3.0
•1•1•0•3•Updated May 3, 2024May 3, 2024
ViVAE_old
Public
Autoencoder-based models for dimension reduction of high-dimensional cytometry and single-cell RNA-seq data based on geometry and nearest-neighbour relations
Python
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Apache License 2.0
•0•3•0•0•Updated Apr 26, 2024Apr 26, 2024
GroupEnc
Public
Encoder with group loss for global structure preservation
Python
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Apache License 2.0
•0•2•0•0•Updated Dec 5, 2023Dec 5, 2023
CytoNorm_note
Public
R code to demonstrate the functionalities of CytoNorm2.0
R
•0•0•0•0•Updated Oct 18, 2023Oct 18, 2023
saeyslab.github.io
Public
HTML
•0•0•0•0•Updated Sep 21, 2023Sep 21, 2023

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