trajectory-inference
From the author
Trajectory inference and cell fate mapping for single-cell and spatial transcriptomics: PAGA graph + diffusion pseudotime (no velocity needed), scVelo RNA velocity (stochastic / dynamical, from spliced/unspliced counts), CellRank 2 terminal states, fate probabilities and lineage drivers, then pseudotime and fates mapped on tissue with a spatial autocorrelation check. Outputs pseudotime, velocity streams, fate probability tables. Imaging panels (Xenium, MERFISH) have no unspliced counts: use PAGA/DPT or the CellRank pseudotime kernel. For a basic PAGA recipe inside a standard scRNA-seq workflow see scanpy-scrna-seq.
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npx skills add jaechang-hits/SciAgent-Skills --skill trajectory-inference -a claude-code
Installs to .claude/skills/trajectory-inference/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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