Gene Expression

This skill enables access to the NCBI Gene Expression Omnibus (GEO), a public repository containing over 264,000 gene expression studies. It provides tools to search for datasets, download microarray and RNA-seq data, parse SOFT/matrix files, and perform expression analysis including differential expression and meta-analysis across studies.

PyDESeq2 is a bioinformatics skill for analyzing bulk RNA-seq count data to identify differentially expressed genes. It provides a complete workflow from data loading through statistical testing (Wald tests with FDR correction), including support for single-factor and multi-factor experimental designs, optional LFC shrinkage, and visualization with volcano/MA plots.