cardamomOT combines gene regulatory network inference and trajectory reconstruction from single-cell temporal snapshots, using a mechanistic optimal transport-based framework building on CARDAMOM.
2024
LTreweighting: Mean Field Langevin algorithm to reconstruct cellular trajectories from sparse lineage tracing data
CARDAMOM (Cell type Analysis from scRna-seq Data achieved from a Mixture MOdel), is a new algorithm for inferring a GRN from timestamped scRNA-seq data, which crucially exploits the notions of metastability and transcriptional bursting.