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# Welcome!  

[<img align="right" width="65%" height="65%" src="https://github.com/pachterlab/gget/blob/main/docs/assets/website_v2_gget_overview.png?raw=true" />](https://raw.githubusercontent.com/pachterlab/gget/main/figures/gget_overview.png)

`gget` is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases.  
<br>
`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.  
<br>
`gget` is part of the [scverse®](https://scverse.org) project and is fiscally sponsored by [NumFOCUS](https://numfocus.org/). If you like `gget` and want to support our mission, please consider making a tax-deductible [donation](https://opencollective.com/scverse/projects/scverse-gget/donate?interval=oneTime&amount=20&contributeAs=me).

> Note: The databases queried by `gget` are continuously updated and may change structure. `gget` modules are [automatically tested](https://github.com/scverse/gget/blob/main/tests/pytest_results.txt) 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](https://github.com/scverse/gget/issues/new/choose).

Missing a database or functionality you’d love to see? [<kbd> <br> Request new feature <br> </kbd>](https://github.com/scverse/gget/issues/new/choose)

# gget modules

These are the `gget` core modules. Click on any module to access detailed documentation.

<table style="width:100%; table-layout:fixed;">
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/8cube.md"><strong>gget 8cube</strong></a><br><span style="font-size:0.85em;">What is the expression of gene X across 8 different mouse strains and tissues?</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/alphafold.md"><strong>gget alphafold</strong></a><br><span style="font-size:0.85em;">Predict 3D protein structure from an amino acid sequence.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/archs4.md"><strong>gget archs4</strong></a><br><span style="font-size:0.85em;">What is the expression of my gene in tissue X?</span></td>
  </tr>
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/bgee.md"><strong>gget bgee</strong></a><br><span style="font-size:0.85em;">Find all orthologs of a gene.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/blast.md"><strong>gget blast</strong></a><br><span style="font-size:0.85em;">BLAST a nucleotide or amino acid sequence.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/blat.md"><strong>gget blat</strong></a><br><span style="font-size:0.85em;">Find the genomic location of a nucleotide or amino acid sequence.</span></td>
  </tr>
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/cbio.md"><strong>gget cbio</strong></a><br><span style="font-size:0.85em;">Explore a gene's expression in the specified cancers.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/cellxgene.md"><strong>gget cellxgene</strong></a><br><span style="font-size:0.85em;">Get ready-to-use single-cell RNA seq count matrices from certain tissues/ diseases/ etc.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/cosmic.md"><strong>gget cosmic</strong></a><br><span style="font-size:0.85em;">Search for genes, mutations, and other factors associated with certain cancers.</span></td>
  </tr>
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/diamond.md"><strong>gget diamond</strong></a><br><span style="font-size:0.85em;">Align amino acid sequences to a reference.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/elm.md"><strong>gget elm</strong></a><br><span style="font-size:0.85em;">Find protein interaction domains and functions in an amino acid sequence.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/enrichr.md"><strong>gget enrichr</strong></a><br><span style="font-size:0.85em;">Check if a list of genes is associated with a specific celltype/ pathway/ disease/ etc.</span></td>
  </tr>
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/info.md"><strong>gget info</strong></a><br><span style="font-size:0.85em;">Fetch all of the information associated with an Ensembl ID.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/muscle.md"><strong>gget muscle</strong></a><br><span style="font-size:0.85em;">Align multiple nucleotide or amino acid sequences to each other.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/mutate.md"><strong>gget mutate</strong></a><br><span style="font-size:0.85em;">Mutate nucleotide sequences based on specified mutations.</span></td>
  </tr>
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/opentargets.md"><strong>gget opentargets</strong></a><br><span style="font-size:0.85em;">Explore which diseases and drugs a gene is associated with.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/pdb.md"><strong>gget pdb</strong></a><br><span style="font-size:0.85em;">Fetch data from the Protein Data Bank (PDB) based on a PDB ID.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/ref.md"><strong>gget ref</strong></a><br><span style="font-size:0.85em;">Get reference genomes from Ensembl.</span></td>
  </tr>
  <tr>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/search.md"><strong>gget search</strong></a><br><span style="font-size:0.85em;">Find Ensembl IDs associated with the specified search word.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/seq.md"><strong>gget seq</strong></a><br><span style="font-size:0.85em;">Fetch the nucleotide or amino acid sequence of a gene.</span></td>
    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/virus.md"><strong>gget virus</strong></a><br><span style="font-size:0.85em;">Filter and fetch global viral sequences and extensive metadata.</span></td>
  </tr>
</table>

<br>  

If you use `gget` in a publication, please [cite*](/gget/en/cite.md):  
```
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](https://doi.org/10.1093/bioinformatics/btac836)

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