FAIR2025_Tutorial_TRACE

This repository provides tools to preprocess mass cytometry (CyTOF) data and compute lower-dimensional embeddings for visualization and analysis with TRACE. It contains a subsample of the original data, preprocessing steps and embedding computations used in the tutorial. If you just want to run TRACE on the dataset, just clone the GitHub repo of TRACE and add the path to ImmuneW_TRACE.h5ad in the data_configs.yaml.

Data availability

The data set used in this example is a mass cytometry data set immunoprofiling women during pregnancy [Van GAssen, S. et al.]. The dataset used for this demonstration contains whole blood samples from two healthy volunteers, both unstimulated and stimulated with Interferonα (IFNα) and Lipopolysacharide (LPS). The data can be downloaded from the data folder in this repository.

Preprocessing

• Data cleaning and transformation
• Marker selection and filtering

Dimensionality reduction

• PCA
• UMAP (n_neighbours=100)
• tSNE (perplexity=100)
• ViVAE (n_epochs=100, lam_mds=10)