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

Update multimodal integration documentation #302

Merged
merged 1 commit into from
Jul 27, 2024
Merged

Update multimodal integration documentation #302

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 12 additions & 5 deletions docs/yaml_docs/pipeline_integration_yml.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -279,14 +279,21 @@ For more information on `bbknn` check the [bbknn documentation](https://bbknn.re
- <span class="parameter">run</span> `Boolean`, Default: True<br>
Set to False if you don't want to run multimodal integration

- <span class="parameter">tools</span> `String`(Comma separated), Default: "WNN"<br>
Method you want to use to run batch correction. Options include: WNN, totalvi and multiVI. You can specify mutiple methods and they will be run simultaneously.
- <span class="parameter">tools</span> `String`(list), Default: "WNN"<br>
Method you want to use to run batch correction. Options include:
- methods with set modalities: totalVI (rna, prot) and multiVI (rna, atac)
- totalvi
- MultiVI
- methods which accept any combination of modalities: MOFA and WNN
- mofa
- WNN

You can specify mutiple methods and they will be run simultaneously.
It makes biological sense to include rna modality if available, which is most informative in terms of cell type differences.

- <span class="parameter">column_categorical</span> `String`(Comma separated), Default: sample_id<br>
This is the column you want to run a batch correction on.
Mltiple columns can be selected simultaneously by providing them as a comma-separated string without spaces.

Extra parameters:
Multiple columns can be selected simultaneously by providing them as a comma-separated string without spaces.

### TotalVI arguments

Expand Down