Add gget joins the scverse ecosystem blog post by muskanhashim · Pull Request #233 · scverse/scverse.github.io

muskanhashim · 2026-07-13T12:17:53Z

Introduce gget as part of the scverse ecosystem, detailing its functionalities and integration for bioinformatics.

netlify · 2026-07-13T12:18:00Z

✅ Deploy Preview for jade-cajeta-1bcca0 ready!

Name	Link
🔨 Latest commit	`54e3852`
🔍 Latest deploy log	https://app.netlify.com/projects/jade-cajeta-1bcca0/deploys/6a550db866131e00088f7b21
😎 Deploy Preview	https://deploy-preview-233--jade-cajeta-1bcca0.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

Updated the description to provide more detail about gget's functionality within the scverse ecosystem.

Zethson

Awesome!

Please put every markdown sentence on its own line. This makes it easier to review and read.
Could we please show an overview figure at the top like in most other blogs of ours. Makes it less dry.

Zethson · 2026-07-13T12:23:18Z

+
+gget was designed with one key idea in mind: one package and import should allow the user to query databases such as Ensembl, UniProt, NCBI, UCSC, AlphaFold, CellxGene, Enrichr, ARCHS4, Open Targets, COSMIC, cBioPortal, and more, without switching to a web browser or writing database-specific boilerplate.
+
+Here's what the standard gget installation and workflow looks like:


Generally a great section but it doesn't show any output. Is it useful as it is?

Zethson · 2026-07-13T12:24:07Z

+gget enrichr BRCA1 TP53 PTEN ATM --database KEGG_2021_Human
+```
+
+## What does this mean for scverse and gget users?


Maybe rephrase this to something like

"gget enables xyz when coupled with scverse tooling" or whatever. Like instead of a question, something concrete. This is not important.

Zethson · 2026-07-13T12:25:45Z

+markers = sc.get.rank_genes_groups_df(adata, group="T cells")["names"].tolist()[:20]
+
+# gget.info() requires Ensembl IDs
+# Use gget.search() to resolve symbols to IDs first


But this isn't used just below or is it?

Zethson · 2026-07-13T12:29:03Z

+
+scverse exists to build a modular, open, and interoperable foundation for single-cell biology. Individual packages focus on what they do best, use shared data structures, and compose naturally with one another. The addition of gget to our ecosystem complements this aspect of our model. This kind of interoperability helps makes tool ecosystems more than the sum of their parts, an important objective for us here at scverse.
+
+Someone studying spatial transcriptomics with Squidpy may want to fetch ligand-receptor protein structures from PDB, or pull disease associations from Open Targets, or BLAST a sequence of interest. The integration of gget makes each of those a one-liner by being the layer helping you handle external reference databases alongside those analyses.


Squidpy should also be a hyperlink

Zethson · 2026-07-13T12:29:26Z

+pip install gget
+```
+
+```shell


I'd not mention uv here

see scverse/cookiecutter-scverse#523 (comment)

I think gget (as a command line tool) would be a good fit for uvx, uv tool install or pipx install.

I think one basically never wants to do uv pip install. It's either uv add to add it to a project, or uv tool install to install it as a global tool.

Well, yes and no. I understand where you're coming from because gget is mostly a CLI tool but the blog even features a usecase where gget is used as a library in jupyter-like setting to fetch datasets from CELLxGENE. So I wouldn't say "never".

But then you'd use uv add, no? Or maybe pip install if you don't use uv at all.
The 'never' was referring to the uv pip command.

I personally don't use uv add as I'm a weirdo that uses uv inside conda environments where I just uv pip install then. But I don't have a strong opinion on this so we can roll with whatever you think is best.

If I remember previous dicsussions with @flying-sheep correctly, using pip install (or uv pip install) on top of existing environments is always a bad idea, as it does not check that all packages are compatible with each other.
uv add does that. Installing all packages at once with pip does as well.

If you install python packages in conda envs it sounds like pixi would be the right choice for you, which, IIRC, is the only tool that checks version constraints of both conda and pypi packages simultaneously.

But to come back to this blog post, I would recommend writing something like

Install the command line tool globally with uv using uv tool install gget or install the python library into your project's virtual environment using pip install gget.

The question remains as in scverse/cookiecutter-scverse#523 if we would like to actively recommend uv to users who may not be using it yet, or if we just keep pip instructions.

Zethson · 2026-07-13T12:30:28Z

+
+The [documentation](https://scverse.org/gget/) covers all modules with worked examples. The [GitHub repository](https://github.com/scverse/gget) is the best place to report issues, propose new database integrations, or contribute.
+
+If you are already using scverse tools for single-cell analysis, gget is a natural addition to your environment. And if you are new to the ecosystem, [scverse.org](https://scverse.org) is the place to start.


Might want to omit that. A bit fluff.
Consider linking to scverse.org/join in any case

Zethson · 2026-07-13T12:30:35Z

+
+---
+
+*gget is an open-source, community-developed tool. Contributions are welcome via the [GitHub repository](https://github.com/scverse/gget).* 


Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

Add gget joins the scverse ecosystem blog post

e0e4822

Introduce gget as part of the scverse ecosystem, detailing its functionalities and integration for bioinformatics.

muskanhashim assigned Zethson Jul 13, 2026

update description of gget in blog post

be1981e

Updated the description to provide more detail about gget's functionality within the scverse ecosystem.

Zethson requested changes Jul 13, 2026

View reviewed changes

muskanhashim and others added 5 commits July 13, 2026 18:01

Update content/blog/2026-gget-joins-scverse.md

a85b893

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

Update content/blog/2026-gget-joins-scverse.md

89a69c9

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

Update content/blog/2026-gget-joins-scverse.md

1155ac7

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

Update content/blog/2026-gget-joins-scverse.md

c5492ed

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

Update content/blog/2026-gget-joins-scverse.md

54e3852

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>


		gget was designed with one key idea in mind: one package and import should allow the user to query databases such as Ensembl, UniProt, NCBI, UCSC, AlphaFold, CellxGene, Enrichr, ARCHS4, Open Targets, COSMIC, cBioPortal, and more, without switching to a web browser or writing database-specific boilerplate.

		Here's what the standard gget installation and workflow looks like:


		scverse exists to build a modular, open, and interoperable foundation for single-cell biology. Individual packages focus on what they do best, use shared data structures, and compose naturally with one another. The addition of gget to our ecosystem complements this aspect of our model. This kind of interoperability helps makes tool ecosystems more than the sum of their parts, an important objective for us here at scverse.

		Someone studying spatial transcriptomics with Squidpy may want to fetch ligand-receptor protein structures from PDB, or pull disease associations from Open Targets, or BLAST a sequence of interest. The integration of gget makes each of those a one-liner by being the layer helping you handle external reference databases alongside those analyses.


		The [documentation](https://scverse.org/gget/) covers all modules with worked examples. The [GitHub repository](https://github.com/scverse/gget) is the best place to report issues, propose new database integrations, or contribute.

		If you are already using scverse tools for single-cell analysis, gget is a natural addition to your environment. And if you are new to the ecosystem, [scverse.org](https://scverse.org) is the place to start.


		---

		gget is an open-source, community-developed tool. Contributions are welcome via the [GitHub repository](https://github.com/scverse/gget).

Uh oh!

Conversation

muskanhashim commented Jul 13, 2026

Uh oh!

netlify Bot commented Jul 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

✅ Deploy Preview for jade-cajeta-1bcca0 ready!

Uh oh!

Zethson left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

netlify Bot commented Jul 13, 2026 •

edited

Loading

Zethson left a comment •

edited

Loading