🖖🏾SPOC: Galaxy Single-cell & sPatial Omics Community of practice

Logo for Galaxy single cell community. People in a circle holding hands standing on a swirling UMAP

We are a mix of users, developers, and trainers providing feedback and energy to improve and expand the Galaxy single cell and spatial omics capabilities.

  • Developers: Are you developing single cell tools in Galaxy, or looking for a place to develop in Galaxy? Do you need users, testers, or just want to make sure you're not wrapping the same tools as someone else!
  • Users: Do you use Galaxy single cell tools for scRNA-seq or beyond? Do you have feedback for us? Want to be a tester of new resources? Do you want to request new resources?
  • Trainers: Do you use Galaxy to train others in single cell analysis? Do you have feedback or requests on how we can support users better now and in the future?
  • Bioinformaticians: Do you do single cell analysis (in Galaxy or outside of it?) Want to contribute to making sure our resources are the best, up-to-date practices in the field? Do you have feedback on how we can do better?

Do you want to impact the future of single cell in Galaxy?

Welcome to 🖖🏾SPOC: the Galaxy Single-cell & sPatial Omics Community of practice!

I'm just trying to learn to analyse my data, how did I get here?

Hello user! You'll be interested in the following resources:

Saying that, we'd absolutely love to have users feedback on their experiences to help us improve. You'd be very welcome to join the Community of Practice to help improve the Galaxy single cell space!

What are the goals of 🖖🏾SPOC?


  • Prevent work duplication
  • Collaborate across pipeline, ensuring users feedback to developers
  • Identify community needs
  • Tool & tutorial development
  • Testing
  • Build & support user community
  • Benchmarking tools and workflows

Who are we looking for?

Anyone with energy! We love hearing from users, developers, trainers, and everyone in between who is using or developing Galaxy for single cell analysis.

How do we function?

Meetings We meet every 4 weeks (alternating USA, EU and AU time zones) for 1 hour.

Our meeting agenda is:

  1. Random intro chatter & introductions
  2. Updates from ClickUp site (what people are working on / asking for help)
    • Help/bugs
    • Status reports & new stuff that’s happening
  3. Other cool stuff (example: Smorgasbord)
  4. Ongoing actions to send out

Emails We send out emails to the mailing list after each meeting, at the mid-way point between meetings, and the day before meetings as a reminder.

Notes We keep rolling notes on a googledoc and monitor our work on ClickUp.

Collaborative Chat Forums When people ask for help or are working across institutes, we set up chat sub-channels to bring them together.

General Chat Forum We have a chat forum to discuss news and ideas, and are represented in the Galaxy Community Reps chat group.

How can you join & other important links

Start by joining our 🖖🏾SPOC Chatroom and introduce yourself! (Or you can just lurk there for a bit!)

Key words

Single-cell Single cell Single-cell RNA-Sequencing Single-cell RNA-seq scRNA-seq snRNA-seq 10x Single cell biology Single cell multiomics ScanPy Seurat AnnData Spatial transcriptomics Spatial omics