Could dropping a few cells change the takeaways from differential expression?

no code implementations • 11 Dec 2023 • Miriam Shiffman, Ryan Giordano, Tamara Broderick

We then overcome the inherent non-differentiability of gene set enrichment analysis to develop an additional approximation for the robustness of top gene sets.

Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data

no code implementations • 28 Nov 2018 • Miriam Shiffman, William T. Stephenson, Geoffrey Schiebinger, Jonathan Huggins, Trevor Campbell, Aviv Regev, Tamara Broderick

Specifically, we extend the framework of the classical Dirichlet diffusion tree to simultaneously infer branch topology and latent cell states along continuous trajectories over the full tree.