gget-genomic-databases

# gget — Unified Genomic Database Access ## Overview gget is a command-line and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequences, protein structures, expression data, and disease associations through a consistent interface. All modules work as both CLI tools and Python functions, returning DataFrames (Python) or JSON/CSV (CLI). ## When to Use - Looking up gene information (names, IDs, descriptions) across species from Ensembl - Retrieving nucleotide or protein sequences for Ensembl gene/transcript IDs - Running BLAST or BLAT searches against standard reference databases - Predicting protein 3D structures with AlphaFold2 from amino acid sequences - Performing gene set enrichment analysis (GO, KEGG, disease terms) via Enrichr - Querying single-cell RNA-seq datasets from CELLxGENE Census - Finding disease and drug associations for a gene target via OpenTargets - Downloading Ensembl reference genomes and annotations for a species - Finding cancer mutations and genomic alterations via cBioPortal or COSMIC - Getting tissue expression and correlated genes from ARCHS4 - For batch processing or advanced BLAST parameters, use `biopython` instead - For programmatic multi-database workflows with rate limiting, use `bioservices` instead ## Prerequisites - **Python packages**: `gget` - **Optional setup**: Some modules require `gget setup <module>` before first use (alphafold, cellxgene, elm, gpt) - **Environment*...