Workflow of data pre-processing method used for MyoMiner. We identified studies that are pertinent to muscle research from GEO and ArrayExpress. Only the studies that provided the raw CEL files proceeded to quality controls. Samples that passed QC were pre-processed with the SCAN algorithm. We thoroughly curated the metadata files and separated them into categories. We used PCA to detect and remove batch effects using the ComBat algorithm. Users have access to muscle tissue and cells gene-pair co-expression, differential co-expression of every category and co-expression networks. All data are available on the MyoMiner web portal.