Individual skill

trajectory-inference

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.

skills/genomics-bioinformatics/spatial-transcriptomics/trajectory-inference/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

What was checked

Matches the observed repository HEAD

Yes

Scanner rules are current

Yes

Repository scan complete

No

Skill scan complete

No

Observed behavior

Network or broad shell

Last checked

Nov 5, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.