Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

scRNAseq - reduce the second session to 1.5/2 hours #11

Open
MichelaTr opened this issue Oct 16, 2023 · 2 comments
Open

scRNAseq - reduce the second session to 1.5/2 hours #11

MichelaTr opened this issue Oct 16, 2023 · 2 comments
Assignees
@ayushi-agrawal-gladstone @MichelaTr
Labels
enhancement New feature or request

Comments

@MichelaTr
Copy link
Contributor

No description provided.

@MichelaTr MichelaTr changed the title scRNAseq - reduce the second session to 2.5/3 hours scRNAseq - reduce the second session to 1.5/2 hours Oct 16, 2023
@ayushi-agrawal-gladstone
Copy link
Contributor

ayushi-agrawal-gladstone commented Oct 17, 2023 •
edited
Loading

  • Use sctransform in the demo instead of log normalize, find variable features and scale data
  • Remove TSNE steps from demo
  • Remove the TSNE notebook from hands-on materials
  • Include a merge step in demo; visualize metadata to show how to look for batch effects
  • Mention in pre-workshop instructions email that the slides might be changed (similar to the email for Intro to RNA-seq)
  • A slide on publicly available data, how to access it and how to clean it up (maybe share a script for clean up?)

@ayushi-agrawal-gladstone
Copy link
Contributor

@MichelaTr @reubenthomas Maybe we can have some time for installation errors (related to all demos) at the end of session 1 and cover some of the topics in session 2?

@ayushi-agrawal-gladstone ayushi-agrawal-gladstone added the enhancement New feature or request label Oct 17, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ayushi-agrawal-gladstone ayushi-agrawal-gladstone

@MichelaTr MichelaTr

Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ayushi-agrawal-gladstone @MichelaTr