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

Plot differentially expressed genes by Biotype #100

Open
grst opened this issue Mar 24, 2023 · 1 comment
Open

Plot differentially expressed genes by Biotype #100

grst opened this issue Mar 24, 2023 · 1 comment
Assignees
Labels
enhancement New feature or request

Comments

@grst
Copy link
Member

grst commented Mar 24, 2023

Description of feature

I find it useful to assess the result of the DE analysis by plotting the number of differentially expressed genes by gene type. If the majority is not protein coding, it is usually a sign that something is not right.

Therefore, I suggest to add a plot like the following to the MultiQC report.

Gene types are typically available from the GTF file.

@grst grst added the enhancement New feature or request label Mar 24, 2023
@pinin4fjords
Copy link
Member

pinin4fjords commented Mar 24, 2023

Sounds good, PRs gratefully received.

I think all the information for that should already be available in the R markdown document's parameters, especially where an Esembl GTF has been supplied as a workflow input (a tabular form of which is then passed to the markdown process).

Note that there's no MulitQC here- just the R markdown.

@ErikaKvalem ErikaKvalem self-assigned this Mar 27, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
No open projects
Status: In Progress
Development

No branches or pull requests

3 participants