Joselyn Chávez

sCCIgen generates synthetic spatial transcriptomics data with known cell-cell interaction features to evaluate analytical tools.

ONTraC uses a graph neural network to analyze spatial transcriptomics data, improving trajectory reconstruction and revealing microenvironment-dependent changes in gene regulation and cell interactions during development.

Giotto Suite provides a modular, open-source framework for analyzing spatial multi-omics data across scales and technologies.

The paper introduces regutools, an R package that enables programmatic access to RegulonDB data for analyzing bacterial regulatory networks within the Bioconductor ecosystem.