ELIXIR Single-Cell Omics Community

Welcome to our Single-Cell Omics (SCO) Community's GitHub repository! Here, we organise and orchestrate information about single-cell and spatial transcriptomics to help researchers using these technologies. Below you can find some quick links to the different parts of the repository where you can add events or curate lists of SCO related tools, training materials, dataset and standards.

News and Upcoming Events

You can list News and Upcoming events to the this file: /docs/pages/news/new_and_events.csv. There, you should simply add a new line and fill the information for all columns.

If you would like to create an SCO Community event, you need to do these steps:

1. Create a markdown file in this folder: /docs/pages/news/events. Please use this naming convention: "YYYYMMDD_Event_Title.md", where "YYYY-MM-DD" is the 1st day of the event incase of multiple days.
2. Then, in this markdown, you can use 20230321_SCO_trainer_workshop.md event as a template as inspiration. In your event, you should add the relevant sections, i.e.:
   • Brief introduction (please polish to maximum 100 words)
   • Dates and city/country
   • Venue details, including Travel information and Accommodation
   • Online Attendance options
   • Participating institution logos/names
   • Footnotes/References.
3. With your Markdown description set, you can add the summary information to the /docs/news/new_and_events.csv file.

About, Training, Tools, Data and News sections

In these page sections, you can add information and lists of resources:

• About: /docs/pages/about/index.md
  • This section is designed to host information about the SCO community itself, how to get involved, how to contribute and additional funding opportunities, either nationally or internationally, including i.e. ELIXIR staff-exchange programme.
• Training: /docs/pages/training/index.md
  • This section contains information about the training materials and resources on SCO. Here, we should include a section of news and events related to training, such as upcoming courses and news regarding training. Also, learning paths and training gaps.
• Tools: /docs/pages/tools/index.md
  • This section will provide list of papers in tool benchmarking, tool overview, some general recommendations and resources that can be used to test and deploy analysis workflows in SCO. It will also contain links to events and news, such as workshops and hackathons.
• Data: /docs/pages/data/index.md
  • This section hosts information about SCO data, including database recommendations for the different omics, data curation guidelines, annotation tools (e.g. UBERON) and help materials to achieve interoperability. News and events related to Data will also be highlighted here.
• News: /docs/pages/news/index.md
  • This section engulfs all News and Events related to SCO communities, including 3rd party events (i.e. HCA GM, ELIXIR AHM, etc) and focused events.