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? Do you want to impact the future of single cell in Galaxy?
Welcome to 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:
- Learning pathway for getting to grips with Galaxy and single cell
- Single cell training material
- Single cell Galaxy instance
- Single cell help forum
- Single cell Galaxy user community chat room
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 the single-cell and spatial omics community of practice?
Goals
- 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 6 weeks (alternating USA, EU and AU time zones) for 1 hour.
Our meeting agenda is:
- Random intro chatter & introductions
- Updates from Trello site (what people are working on / asking for help)
- Help/bugs
- Status reports & new stuff that’s happening
- Other cool stuff (example: Smorgasbord)
- 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 Trello.
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 SC Community of Practice Chatroom and introduce yourself! (Or you can just lurk there for a bit!)
- Mailing list
- Trello site
- SC-CoP Google Calendar <-- Subscribe!
- ICal link for non-google users
- Meeting Notes doc <--- There's a section here called 'New here?' that gives tips on how to start contributing as well!
- User Matrix Channel
- SC Community of Practice Chatroom
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