Explore @saeyslab Open Source projects

Saeys Lab (@saeyslab)

saeyslab

Stars
568
Global Org. Rank 21,766 (Top 7 %)
Registered about 8 years ago
Most used languages

R
53.3 %

Python
23.3 %

HTML
10.0 %

Jupyter Notebook
10.0 %

JavaScript
3.3 %
Location 🇧🇪 Belgium
Country Total Rank 266
Country Ranking

R
2

HTML
25

Jupyter Notebook
64

Python
410

JavaScript
1,107

nichenetr

NicheNet: predict active ligand-target links between interacting cells

multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

CytoNorm

R library to normalize cytometry data

moduledetection-evaluation

Jupyter Notebook

FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data

FlowCytometryScripts

spotless-benchmark

A repository for benchmarking spatial deconvolution and mapping tools

brainimmuneatlas

Overview of the scripts used to analyse the brainimmuneatlas data

PeacoQC

Peak-based selection of high quality cytometry data

DeepLearning_for_ImagingFlowCytometry

A framework around Tensorflow-Keras that makes it easy to train and evaluate any deep learning architecture on imaging flow cytometry data.

triwise

An R package to analyze and visualize gene expression differences in three biological conditions

NicheNet_LiverCellAtlas

Scripts used for the Differential NicheNet analyses in the Liver Atlas paper Guilliams et al., Cell 2022

FlowSOM_Python

The complete FlowSOM package known from R, now available in Python!

MFs_peripheralCentralNerveSystem

Scripts of Ydens et al. Nature Neuroscience. 2020

dambi-hpc-guide

Basic and Advanced usage of High-Performance Computing in Bioinformatics

binary-ivap

Jupyter Notebook

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

FlowSOM_protocol

R code to demonstrate the FlowSOM analysis pipeline.

synthspot

synthvisium: package to generate synthetic Visium-like spot data

multivap

Multiclass generalization of the binary IVAP defense against adversarial examples

Jupyter Notebook

ViScore

Unsupervised benchmarking and supervised explanatory evaluation measures for dimensionality reduction of single-cell data

GroupEnc

Encoder with group loss for global structure preservation

muscatWrapper

Easy muscat differential expression analysis and visualization

Roquin-1-hyperinflammation

Code to generate some of the results described by Tavernier et al.

ComputationalCytometry

Workshop computational cytometry

Kiss_et_al_CellularImmunologyReview

R code to replicate the tSNE and FlowSOM figures

hydra_hpc_example

Hydra HPC example

sc_hackathon_2023

Ghent hackathon on Python/R interoperability for single cell and spatial bioinformatics

portal

Site for https://saeyslab.github.io/portal/

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.

FlowSOM_workshop

Example usage of the FlowSOM package