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.

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

Provide context in vignettes #71

Open
7 tasks
lwaldron opened this issue Jul 4, 2023 · 1 comment
Open
7 tasks

Provide context in vignettes #71

lwaldron opened this issue Jul 4, 2023 · 1 comment
Assignees
Labels
documentation Improvements or additions to documentation

Comments

@lwaldron
Copy link
Member

lwaldron commented Jul 4, 2023

The vignettes would benefit a lot from addition of prose from the manuscript that provides context for what the dataset provides and how it can be used. For example, if someone is looking for a dataset where they could use one omics type for cell type identification and RNA-seq for differential expression analysis between cell types, you couldn't figure out what might be an appropriate dataset from the documentation which currently focuses just on outputs of R commands. This documentation enhancement could be made just by copying relevant parts of the manuscript into the vignette of each dataset, and citing the manuscript. @kbeckenrode do you think you could take this on and submit a PR?

  • seqFISH.Rmd
  • SCoPE2.Rmd
  • ECCITEseq.Rmd
  • scMultiome.Rmd
  • GTseq.Rmd
  • scNMT.Rmd
  • CITEseq.Rmd
@lwaldron lwaldron added the documentation Improvements or additions to documentation label Jul 4, 2023
@lwaldron
Copy link
Member Author

lwaldron commented Jul 4, 2023

Ideally this would also include the table for each dataset, translated into Markdown (e.g. using one of the Markdown table generators), as well as the cell filtering and annotations information from Table 9.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
documentation Improvements or additions to documentation
Projects
None yet
Development

No branches or pull requests

2 participants