Saeys Lab

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58 repositories

harpy
Public
https://harpy.readthedocs.io/en/latest/
Python
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Other
•2•12•12•0•Updated Jan 28, 2025Jan 28, 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
•4•14•4•1•Updated Jan 24, 2025Jan 24, 2025
spotless-benchmark
Public
A repository for benchmarking spatial deconvolution and mapping tools
R
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MIT License
•2•28•0•0•Updated Jan 24, 2025Jan 24, 2025
napari-sparrow
Public
https://sparrow-pipeline.readthedocs.io/en/latest/
Python
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Other
•0•23•11•0•Updated Jan 17, 2025Jan 17, 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
•15•133•10•0•Updated Jan 14, 2025Jan 14, 2025
nichenet_protocol
Public
HTML
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MIT License
•0•0•0•0•Updated Dec 18, 2024Dec 18, 2024
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•3•0•0•Updated Dec 9, 2024Dec 9, 2024
hydra_hpc_example
Public
Hydra HPC example
python hpc slurm hydra
Python
•0•4•0•0•Updated Dec 9, 2024Dec 9, 2024
CytoNorm
Public
R library to normalize cytometry data
R
•8•33•29•0•Updated Oct 28, 2024Oct 28, 2024
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 Oct 21, 2024Oct 21, 2024
CytoBright
Public
Estimate Stain Index for single stained cytometry files.
R
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GNU General Public License v3.0
•0•2•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
•0•1•0•0•Updated Sep 10, 2024Sep 10, 2024
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
•120•510•17•0•Updated Sep 5, 2024Sep 5, 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
ComputationalCytometry
Public
Workshop computational cytometry
R
•0•2•0•0•Updated Jul 5, 2024Jul 5, 2024
FlowSOM
Public
Using self-organizing maps for visualization and interpretation of cytometry data
R
•8•25•5•0•Updated Jul 3, 2024Jul 3, 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
•
MIT License
•1•0•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•3•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
marble-sorter-ui
Public
Interface for the marble sorter
Python
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MIT License
•0•0•0•0•Updated Mar 11, 2024Mar 11, 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
Liechti_et_al_TwinStudy
Public
Code used to generate the results described in Liechti et al.
R
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GNU General Public License v3.0
•0•2•0•0•Updated Sep 20, 2023Sep 20, 2023
sc_hackathon_2023
Public
Ghent hackathon on Python/R interoperability for single cell and spatial bioinformatics
MIT License
•0•1•0•0•Updated Sep 19, 2023Sep 19, 2023
ViScoreR
Public
Cell population-level evaluation of low-dimensional embeddings of labelled biological single-cell datasets
R
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MIT License
•0•0•0•0•Updated Sep 12, 2023Sep 12, 2023
PeacoQC
Public
Peak-based selection of high quality cytometry data
R
•9•15•6•0•Updated Aug 24, 2023Aug 24, 2023