Preregistered reanalysis of a dystroglycan glycan-biosynthesis transcript score in disuse, recovery and training: result tables, analysis code and screening records

Files supporting a preregistered external test of one fixed eight-gene transcript module (writer8: POMGNT2, POMK, B3GALNT2, FKTN, FKRP, RXYLT1, B4GAT1, LARGE1; the enzymes that build matriglycan on alpha-dystroglycan) in public human and rodent skeletal-muscle transcriptomes of disuse, recovery and training. The protocol (version 1.0) and Amendment A1 were registered on OSF before the search, screening and any access to expression data (https://doi.org/10.17605/OSF.IO/GDVJH); Amendments A2 and A3 were registered before data access (https://doi.org/10.5281/zenodo.23204360). The post hoc plans, Amendments A4 and A5, were added to the registration before the parts that read expression data again were run (https://doi.org/10.5281/zenodo.23851939 and https://doi.org/10.5281/zenodo.23855491). The archive holds the result tables of the registered analysis (pooled estimates, gates, multiplicity families, per-comparison effect sizes, leave-one-cohort-out, composition sensitivity, alternative arms, gene-level description, per-unit scores, descriptive comparisons), the registered analysis code with its synthetic tests, the data readers and download manifests with the SHA-256 of every input, the read-reprocessing record (nf-core/rnaseq 3.27.0, Salmon, Ensembl 116), the search, screening and extraction records with the author's confirmation and adjudication workbooks, the exposure log of every data access after registration, and the scripts that build the tables, figures and reference table of the accompanying article. Version 2.0 adds the post hoc analyses, which are not registered and not blind and change no registered result: Amendment A4 Part 1 (from the registered result files), Part 2 (programmes, an expression-matched random gene-set null, alternative scores and ranking universes) and the three checks of Amendment A5, each with its code, synthetic tests, outputs, manifest and run record; the record of a post hoc scan of public glycoproteomics data; and the scripts and outputs of the tables and figures of the second version of the article. The scoring code of version 1.0.0 (https://doi.org/10.5281/zenodo.22884854) is required to rerun the analysis. Not included: expression data (all public at GEO, ArrayExpress/ENA and MoTrPAC; fetch scripts and checksums are included), the manuscript text, and the Methods sections of source publications read during verification. MANIFEST.sha256 lists the SHA-256 of every file; README.md describes the contents and how to reproduce the article's tables and figures. Version 1.0 was prepared but never published; this is the first public version.