Seurat: CCA for cross-species

Created on 6 Jul 2018 · 9Comments · Source: satijalab/seurat

I was interested in running CCA for cross species (human and mouse). I looked for the Nat Biotech paper and its supplementary. The only code I could find is "immune_workflow" that runs CCA for integration of IFNB stimulated and control PBMCs. Would it be similar code (in principle) to run cross-species CCA or something different. Need some assistance!!

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parveenkgit

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Me too. Thanks so much!

StanleyYang01 on 14 Aug 2019

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All 9 comments

I would second this, it would be great to have a cross-species integration vignette or at least the code for the example in the paper made available. There are additional issues with cross-species work that aren't addressed in the current (excellent) vignette and an example would be of use to the community.

lazappi on 8 Jul 2018

👍3

Of course - we're happy to share this (I believe it was on the website originally but then taken down for simplicity when we restructured). We have a couple people traveling, but will post when they are back.

The workflow is identical to the immune example on the website. While there are additional issues with cross-species (particularly for non-homologous gene names), in the manuscript we just address these by only considering genes with identical names in both species (and treating theses as homologous), but we're working on more advanced solutions.

satijalab on 8 Jul 2018

Hey Seurat team, any update with the code requested?

parveenkgit on 20 Jul 2018

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