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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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How do I combine multiple samples in giotto? #110

Closed smk5g5 closed 3 years ago

smk5g5 commented 3 years ago

Is there a way to combine multiple samples in giotto? I was looking at the manual and could not find anything regarding that I was wondering if it is possible to do this in giotto? if not is there a workaround for the same?

Thank you!

RubD commented 3 years ago

Hi @smk5g5 sorry for the late reply. This is not possible in the current master branch of Giotto, however you can do this (and much more) if you use the suite branch. The branch is fully functional, but we're still making changes and improvements and there might be some more bugs. We're happy to help if you run into any issues.

You can simply install the suite branch with the command devtools::install_github("RubD/Giotto@suite"). I'm also attaching an example script (.txt format for github reasons) for the prostate normal & cancer FFPE visium dataset. In this example I'm showing you how to join giotto objects and also how to perform data integration (using Harmony) if that would be of interest. Best, Ruben

Visium_FFPE_prostate_normal_cancer.txt

pcantalupo commented 6 months ago

The link is broken. Can you provide an updated link? Thank you

josschavezf commented 6 months ago

@pcantalupo here is the updated link https://drieslab.github.io/Giotto_website/articles/visium_prostate_integration.html