Pinned Repositories
brainimmuneatlas
Overview of the scripts used to analyse the brainimmuneatlas data
CytoNorm
R library to normalize cytometry data
FlowCytometryScripts
FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data
moduledetection-evaluation
multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
napari-sparrow
nichenetr
NicheNet: predict active ligand-target links between interacting cells
PeacoQC
Peak-based selection of high quality cytometry data
spotless-benchmark
A repository for benchmarking spatial deconvolution and mapping tools
Saeys Lab's Repositories
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
saeyslab/CytoNorm
R library to normalize cytometry data
saeyslab/spotless-benchmark
A repository for benchmarking spatial deconvolution and mapping tools
saeyslab/FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data
saeyslab/napari-sparrow
saeyslab/PeacoQC
Peak-based selection of high quality cytometry data
saeyslab/FlowSOM_Python
The complete FlowSOM package known from R, now available in Python!
saeyslab/harpy
saeyslab/synthspot
synthspot: package to generate synthetic Visium-like spot data
saeyslab/ViScore
Single-cell dimensionality reduction evaluation and benchmarking toolkit
saeyslab/ViVAE_old
Autoencoder-based models for dimension reduction of high-dimensional cytometry and single-cell RNA-seq data based on geometry and nearest-neighbour relations
saeyslab/CytoBright
Estimate Stain Index for single stained cytometry files.
saeyslab/GroupEnc
Encoder with group loss for global structure preservation
saeyslab/Liechti_et_al_TwinStudy
Code used to generate the results described in Liechti et al.
saeyslab/cifconvert
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.
saeyslab/ComputationalCytometry
Workshop computational cytometry
saeyslab/hydra_hpc_example
Hydra HPC example
saeyslab/sc_hackathon_2023
Ghent hackathon on Python/R interoperability for single cell and spatial bioinformatics
saeyslab/VIB_Hackathon_June_2024
Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8T
saeyslab/ViVAE
Single-cell dimensionality reduction toolkit
saeyslab/CytoNorm_note
R code to demonstrate the functionalities of CytoNorm2.0
saeyslab/marble-sorter-ui
Interface for the marble sorter
saeyslab/nichenet_training
saeyslab/spatial_ccc_experiments
saeyslab/Computational_pipeline_EuroFlow_AML
saeyslab/ExtractInfinicyt
Script to extract fcs files and gating information from infinicyt .CYT files
saeyslab/nichenet_protocol
saeyslab/saeyslab.github.io
saeyslab/ViScoreR
Cell population-level evaluation of low-dimensional embeddings of labelled biological single-cell datasets