00_overview.md

STAR Suite Codespaces

These guides help you try STAR Suite in GitHub Codespaces with small public datasets.

What is ready now

• Bulk: ready
• SLAM: ready
• Single-cell input builder: ready
• Perturb: still being worked on
• Flex: still being worked on

Pick a starting point

• If you are new to this:
  • start with Optional setup: small demo reference
  • then run Bulk
  • then try SLAM
• If you already use STAR or Cell Ranger:
  • read If you already use STAR or Cell Ranger
  • then jump straight to the guide you want
• If you already have your own STAR index:
  • skip setup
  • go straight to Bulk or SLAM
• If you want to try perturb or Flex later:
  • first build the small shared single-cell input with Single-cell input for perturb and Flex

Guides

• Optional setup: small demo reference
• Bulk
• SLAM
• Single-cell input for perturb and Flex
• Perturb (work in progress)
• Flex (work in progress)
• If you already use STAR or Cell Ranger
• Using your own data

Notes

• The Codespaces setup tries to install a small walkthrough extension automatically.
• If that does not happen, open the Command Palette and run STAR-suite: Open Codespaces Walkthrough.
• You can replace the demo reference, STAR index, and input files with your own at any time.
• See Using your own data.