Have you ever run Monocle3 and ended up with a tangled mess of trajectories on your UMAP plot? You’re not alone. Monocle3 is one of the most popular tools for trajectory inference in single-cell RNA-seq, but its default settings can sometimes produce overly complex graphs — full of short loops, spurious branches, and paths that don’t make biological sense. In this post, we’ll break down: ✅ Final Thoughts Monocle3 is… Continue Reading... "Optimizing Trajectory Inference in Monocle3: Best Practices for Cleaning Pseudotime Paths"
Optimizing Trajectory Inference in Monocle3: Best Practices for Cleaning Pseudotime Paths
