Sofie Van Gassen

Interpretable models for scRNA-seq data embedding with multi-scale structure preservation

This paper introduces two tools for improving the trustworthiness of single-cell dimensionality reduction by enhancing quality metrics and multi-scale structure preservation.

CytoScan: Automated detection of technical anomalies for cytometry quality control

CytoScan detects technical anomalies in cytometry data by identifying outliers and novelties, improving quality control for reliable analyses.

CytoNormPy enables a fast and scalable removal of batch effects in cytometry datasets.

CytoNormPy provides a fast Python implementation of CytoNorm for removing batch effects in cytometry data, with added clustering and visualization tools.

An optimal transport-based low-dimensional visualization framework for high-parameter flow cytometry

This paper introduces an optimal transport-based framework for visualizing high-parameter flow cytometry data, providing biologically consistent layouts and enabling quantitative analysis of population changes.

Systemic autoimmune disease patients' blood immunome reveals specificities and commonalities among different diagnostic entities

The paper uses immunophenotyping to identify patient subgroups in systemic autoimmune diseases, revealing shared immunophenotypes and cytokine signatures across different diagnoses.