Ncbi

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.

This skill enables querying the NCBI Gene database for gene annotation and functional analysis. It provides Python scripts to search genes by symbol or ID, retrieve detailed gene metadata including RefSeqs, GO annotations, chromosomal locations, and phenotypes, and perform efficient batch lookups with built-in rate limiting.

A comprehensive guide for accessing NCBI's ClinVar database to query clinical significance of human genetic variants. Provides documentation on searching variants by gene/position, interpreting pathogenicity classifications (ACMG/AMP guidelines), downloading bulk data via FTP, and annotating VCF files with clinical significance.

A comprehensive reference skill for the Biopython library, providing documentation and code examples for computational molecular biology tasks. Covers sequence manipulation, NCBI database access (GenBank, PubMed), BLAST searches, protein structure analysis, phylogenetics, and advanced features like motif analysis and restriction enzyme mapping.