Detecting commitment switches in scRNA-seq differentiation trajectories: a Claw4S skill for understanding development and informing iPSC protocol design

This deposition contains the reproducibility artifacts for "Detecting commitment switches in scRNA-seq differentiation trajectories: A Claw4S skill for understanding development and informing iPSC protocol design" (Claw4S submission, April 2026). The companion research note describes a method for detecting gene expression commitment switches along single-cell RNA-seq differentiation trajectories, applied to a 299,552-cell integrated human cardiac dataset spanning fetal and adult development. The method yields 194 fate-weighted switches stratified into five transcription factor support tiers, with a core_consistent subset (n=35) constituting the primary biology claim. Contents: 07_after_trajectory.h5ad (~2.17 GB): AnnData checkpoint from the locked cardiac_switches pipeline. 299,552 cells x 27,776 genes, integrated fetal (GSE216019, Knight-Schrijver et al. 2022) and adult (Heart Cell Atlas) heart data. Includes scVI latent embedding, diffusion pseudotime, CellRank GPCCA terminal state memberships and fate probabilities, and post-hoc-corrected terminal state annotations. collectri_human_20260418.tsv (~2.4 MB): Frozen CollecTRI human TF-target network snapshot (42,990 edges, 1,185 TFs) used for decoupleR activity inference. Shipped pinned for Arm 1 reproducibility; users adapting the pipeline should refresh via COLLECTRI_MODE='fresh' and commit the dated snapshot generated by the pipeline. README.md: Contents index, SHA-256 checksums, pipeline provenance (GitHub commit 896c863), and pointer to the execution contract (SKILL.md) for reviewing Claws. Usage: The companion SKILL.md in the cardiac_switches GitHub repository defines a Claw execution contract for downloading this deposition and re-running the 07c -> 08 -> 08b -> 09 -> 09b downstream pipeline from the checkpoint. Outputs (194-switch CSV, decoupleR activity matrices, figures) are regenerated by the Claw and are intentionally not included here to preserve the integrity of the execution contract. Companion research note: [clawRxiv DOI, to be added after submission]. Source code: https://github.com/HangryPeteSays/cardiac_switches (commit 896c863).