MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis

Abstract

SUMMARY\nThe rapid advances of omics technologies have generated abundant genomic data in public repositories and effective analytical approaches are critical to fully decipher biological knowledge inside these data. Meta-analysis combines multiple studies of a related hypothesis to improve statistical power, accuracy and reproducibility beyond individual study analysis. To date, many transcriptomic meta-analysis methods have been developed, yet few thoughtful guidelines exist. Here, we introduce a comprehensive analytical pipeline and browser-based software suite, called MetaOmics, to meta-analyze multiple transcriptomic studies for various biological purposes, including quality control, differential expression analysis, pathway enrichment analysis, differential co-expression network analysis, prediction, clustering and dimension reduction. The pipeline includes many public as well as >10 in-house transcriptomic meta-analytic methods with data-driven and biological-aim-driven strategies, hands-on protocols, an intuitive user interface and step-by-step instructions.\n\n\nAVAILABILITY AND IMPLEMENTATION\nMetaOmics is freely available at https://github.com/metaOmics/metaOmics.\n\n\nSUPPLEMENTARY INFORMATION\nSupplementary data are available at Bioinformatics online.