An Integrated Reference Atlas of Human Skeletal Muscle

This repository contains the processed data and supporting resources for the human skeletal muscle cell atlas described in the associated publication. The atlas comprises 753,037 cells and nuclei, 124,415 expression features, from seven source studies. The deposit includes: A Seurat v5 RDS object containing normalized expression, the retained heterogeneous count-like matrix, curated cell metadata, feature metadata and five dimensional reductions. An H5AD object containing normalized expression in X, curated observation and feature metadata, and the corresponding PCA, Harmony, RPCA and UMAP embeddings. The count-like matrix was intentionally omitted from the H5AD to avoid unnecessary duplication. Observation- and feature-level metadata, a data dictionary, object-structure documentation, usage notes, validation information, a file manifest and SHA-256 checksums. app.R, which contains the application logic and interface code used to assemble the Shiny application described in the publication. The celltype_top500_markers R object, containing the 500 highest-ranked marker genes for each cell population together with the corresponding ranking statistics. Each observation is linked to its source through the hierarchy cell_id → library_id → specimen_id → donor_id → source_study. The complete mapping is provided in cell_metadata.tsv.gz, allowing the data to be interpreted . The deposit is openly accessible and contains no direct personal identifiers. Curated metadata, annotations, application code and documentation are released under the terms specified in LICENSE.txt. Please reach out if you have additional questions.