saeyslab/brainimmuneatlas

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Language
R
Created over 5 years ago
Updated over 1 year ago

saeyslab/brainimmuneatlas

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Overview of the scripts used to analyse the brainimmuneatlas data

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

napari-sparrow

https://sparrow-pipeline.readthedocs.io/en/latest/

PeacoQC

Peak-based selection of high quality cytometry data

FlowSOM_Python

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

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

MFs_peripheralCentralNerveSystem

Scripts of Ydens et al. Nature Neuroscience. 2020

dambi-hpc-guide

Basic and Advanced usage of High-Performance Computing in Bioinformatics

harpy

ViScore

Single-cell dimensionality reduction evaluation and benchmarking toolkit

Jupyter Notebook

FlowSOM_protocol

R code to demonstrate the FlowSOM analysis pipeline.

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

ComputationalCytometry

Workshop computational cytometry

synthspot

synthvisium: package to generate synthetic Visium-like spot data

multivap

Multiclass generalization of the binary IVAP defense against adversarial examples

Jupyter Notebook

VIB_Hackathon_June_2024

Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8T

Jupyter Notebook

GroupEnc

Encoder with group loss for global structure preservation

ViVAE

Single-cell dimensionality reduction toolkit

Jupyter Notebook

muscatWrapper

Easy muscat differential expression analysis and visualization

portal

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

Roquin-1-hyperinflammation

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

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

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