Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against…
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and…
Use when a user needs to find the right skill for a research task, especially when the task can be mapped to Concepts and Theory, Research Capabilities, Methods and Techniques, Software and Tools, Instruments and Equipment, Data and Resources, Workflows, or Standards and Guidelines, or when the research stage belongs…
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