Source data and code for: A pan-pediatric cancer atlas of alternative splicing regulation and splicing-derived neoantigens

Complete source data, analysis code, and figure-generation materials for the manuscript "A pan-pediatric cancer atlas of alternative splicing regulation and splicing-derived neoantigens" (Tang M, Chen X, Yang S, Duan Q). Study summary. Using the checksum-verified OpenPedCan release v15 (3,818 pediatric tumors across 23 histologies and 283 xenograft models), this resource profiles 211 splicing factors, catalogues 434,755 alternative splicing events, and tests splicing-derived antigen candidates at three levels: MHC-I presentation, junction-level detectability across 17,382 GTEx normal transcriptomes, and pediatric CRISPR dependency (DepMap 22Q2). Package contents (50 files, 142 MB zipped): 01_cohort/ — cohort assembly: sample lists, per-histology counts, PDX inventory 02_sf_expression/ — validated 211-factor catalogue; per-histology restriction calls against pooled pediatric tumours and GTEx normal tissue 03_sf_mutations/ — filtered MAF of splicing-factor alterations (2,628 specimens). Note: U2AF1 rows lie inside the GRCh38 chr21p artifact interval (chr21:43,035,875-43,187,577; Miller et al., J Mol Diagn 2022;24:219-223) and are not interpretable as hotspot absence 04_event_catalog/ — streaming rMATS catalogue: 434,755 events × 4,124 pediatric samples (event_catalog_long.tsv.gz), restriction calls, antigen-relevant subset 05_pediatric_vs_adult/ — pediatric-versus-adult comparisons plus library-matched sensitivity re-analysis 06_neoantigen/ — junction-peptide construction (full event rows; 1,341 event-peptide pairs), all 34,290 peptide-allele MHC predictions, ranked 26-candidate list 07_depmap/ — CRISPR gene-effect summaries and tiered factor–gene priority table 08_immune/ — per-sample and per-histology immune scores 09_isoform/ — transcript-usage shifts of the 211 factors revision_ctd2/ — post-review analyses: frame-anchored sensitivity ranking, junction-level normal-tissue detectability (GTEx v8 junction matrix, 17,382 transcriptomes), library-matched comparison code/ — pipeline_snapshot.tar.gz (complete pipeline, run logs, docs) and manuscript_source.tar.gz (LaTeX source and figures) figures_source/ — per-figure code, data, and environment snapshots provenance/ — OpenPedCan release md5 manifest checksums.sha256, MANIFEST.txt, README.md — integrity and documentation Data sources (all public): OpenPedCan v15 (public S3 d3b-openaccess-us-east-1-prd-pbta/open-targets/v15/, every file verified against the release md5sum.txt); GTEx v8 (dbGaP phs000424.v8.p2, junction read-count matrix GTEx_Analysis_2017-06-05_v8_STARv2.5.3a_junctions.gct.gz); TCGA Pan-Cancer via GDC/OpenPedCan harmonisation; DepMap 22Q2 via Bioconductor ExperimentHub EH7554/EH7556/EH7558. Integrity. checksums.sha256 lists one SHA-256 per file. Every numeric value in the manuscript derives from these tables, and each table is reproducible from the scripts in code/pipeline_snapshot.tar.gz with the included run logs.