Achille Nazaret

AMICI estimates cell-cell interaction length scales and links communication to gene programs in spatial transcriptomic data.

Decipher is a deep generative model that integrates single-cell RNA-seq data to visualize and characterize transitions between normal and perturbed cell states across different diseases.

This study uses spatiotemporal single-cell analysis to track T cell clonal dynamics and phenotypic plasticity in GVHD, revealing links between TCR features, clonal expansion, and disease severity.

Starfysh integrates spatial transcriptomics and histology to analyze tumor microenvironments, identifying disease-specific spatial hubs and immune interactions in breast cancers.

scvi-tools provides a Python package for probabilistic analysis of single-cell omics data, offering standardized interfaces and extensible tools for various analysis tasks.