Welcome!
gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases.
gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.
Note: The databases queried by
ggetare continuously updated and may change structure.ggetmodules are automatically tested twice weekly and updated as needed. If you encounter an issue, first upgrade to the latest version with pip install --upgrade gget. If the issue persists, please report it.
Missing a database or functionality you’d love to see?
Request new feature
gget modules
These are the gget core modules. Click on any module to access detailed documentation.
| gget 8cube What is the expression of gene X across 8 different mouse strains and tissues? |
gget alphafold Predict 3D protein structure from an amino acid sequence. |
gget archs4 What is the expression of my gene in tissue X? |
| gget bgee Find all orthologs of a gene. |
gget blast BLAST a nucleotide or amino acid sequence. |
gget blat Find the genomic location of a nucleotide or amino acid sequence. |
| gget cbio Explore a gene's expression in the specified cancers. |
gget cellxgene Get ready-to-use single-cell RNA seq count matrices from certain tissues/ diseases/ etc. |
gget cosmic Search for genes, mutations, and other factors associated with certain cancers. |
| gget diamond Align amino acid sequences to a reference. |
gget elm Find protein interaction domains and functions in an amino acid sequence. |
gget enrichr Check if a list of genes is associated with a specific celltype/ pathway/ disease/ etc. |
| gget info Fetch all of the information associated with an Ensembl ID. |
gget muscle Align multiple nucleotide or amino acid sequences to each other. |
gget mutate Mutate nucleotide sequences based on specified mutations. |
| gget opentargets Explore which diseases and drugs a gene is associated with. |
gget pdb Fetch data from the Protein Data Bank (PDB) based on a PDB ID. |
gget ref Get reference genomes from Ensembl. |
| gget search Find Ensembl IDs associated with the specified search word. |
gget seq Fetch the nucleotide or amino acid sequence of a gene. |
gget virus Filter and fetch global viral sequences and extensive metadata. |
If you use gget in a publication, please cite*:
Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836
Read the article here: https://doi.org/10.1093/bioinformatics/btac836
