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nichenetr
NicheNet: predict active ligand-target links between interacting cellsmultinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics dataCytoNorm
R library to normalize cytometry datamoduledetection-evaluation
FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry dataFlowCytometryScripts
spotless-benchmark
A repository for benchmarking spatial deconvolution and mapping toolsbrainimmuneatlas
Overview of the scripts used to analyse the brainimmuneatlas dataPeacoQC
Peak-based selection of high quality cytometry dataDeepLearning_for_ImagingFlowCytometry
A framework around Tensorflow-Keras that makes it easy to train and evaluate any deep learning architecture on imaging flow cytometry data.napari-sparrow
FlowSOM_Python
The complete FlowSOM package known from R, now available in Python!triwise
An R package to analyze and visualize gene expression differences in three biological conditionsNicheNet_LiverCellAtlas
Scripts used for the Differential NicheNet analyses in the Liver Atlas paper Guilliams et al., Cell 2022MFs_peripheralCentralNerveSystem
Scripts of Ydens et al. Nature Neuroscience. 2020dambi-hpc-guide
Basic and Advanced usage of High-Performance Computing in Bioinformaticsbinary-ivap
ViVAE_old
Autoencoder-based models for dimension reduction of high-dimensional cytometry and single-cell RNA-seq data based on geometry and nearest-neighbour relationsFlowSOM_protocol
R code to demonstrate the FlowSOM analysis pipeline.synthspot
synthvisium: package to generate synthetic Visium-like spot datamultivap
Multiclass generalization of the binary IVAP defense against adversarial examplesGroupEnc
Encoder with group loss for global structure preservationmuscatWrapper
Easy muscat differential expression analysis and visualizationportal
Site for https://saeyslab.github.io/portal/Roquin-1-hyperinflammation
Code to generate some of the results described by Tavernier et al.ComputationalCytometry
Workshop computational cytometryKiss_et_al_CellularImmunologyReview
R code to replicate the tSNE and FlowSOM figureshydra_hpc_example
Hydra HPC examplesc_hackathon_2023
Ghent hackathon on Python/R interoperability for single cell and spatial bioinformaticscifconvert
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.FlowSOM_workshop
Example usage of the FlowSOM packageVIB_Hackathon_June_2024
Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8TLove Open Source and this site? Check out how you can help us