scPath: Pathway-informed single-cell atlas harmonization software and research archive

Restricted software, code, prepared inputs, historical outputs, and original analysis notebooks accompanying the manuscript 'Pathway-informed harmonization of single-cell atlases across biological contexts.' This deposit contains the English scPath software snapshot and runnable CEL-Seq2-to-10x Chromium V2 example; separate archives for the original cross-platform PBMC, cross-tissue, cross-disease pancreas, bone-marrow aging, and PDAC/NACT studies; and a shared archive with byte-identical active MPNN_SelfDistill core modules and human/mouse Reactome and KEGG GMT pathway files. The experiment archives retain their original notebooks and saved outputs; results were not recomputed for this release. Prepared inputs and selected outputs are included. Large model checkpoints, regenerable graph caches, raw FASTQ, and full public parent atlas downloads are omitted. File-level source paths and SHA-256 values are recorded in FILE_MANIFEST.csv; archive checksums are in SHA256SUMS. All record files are restricted and reviewed by the record owner. Approval grants access only; redistribution, modification, or reuse is not permitted without prior written permission from the rights holders. All rights are reserved. Upstream dataset and third-party resource terms continue to apply. The article author list and affiliations were supplied by the corresponding project owner.