COT: an efficient Python tool for detecting marker genes among many subtypes
Lu, Y.; Wu, C.-T.; Parker, S. J.; Chen, L.; Saylor, G.; Van Eyk, J. E.; Herrington, D. M.; Wang, Y.
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We develop an accurate and efficient method to detect marker genes among many subtypes using subtype-enriched expression profiles. We implement a Cosine based One-sample Test (COT) Python software that is easy to use and applicable to multi-omics data. We demonstrate the performance and utility of COT on gene expression and proteomics data acquired from tissue or cell subtypes. Formulated as a one-sample test with Cosine similarity test statistic in scatter space, the detected de novo marker genes will allow biologists to perform a more comprehensive and unbiased molecular characterization, deconvolution and classification of complex tissue or cell subtypes.
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