search

saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
169 stars 30 forks source link

Use of LIANA with a different species #23

Closed Goultard59 closed 2 years ago

Goultard59 commented 2 years ago

Hello,

I would like to know, if it's possible to obtain and use orthologous protein id from another species (pig).

Thanks

Regards, Adrien

dbdimitrov commented 2 years ago

Hi Adrien,

Please check this issue as it answers your question: https://github.com/saezlab/liana/issues/22#issuecomment-928067888

I had a look and the corresponding database on ensmbl for pogs is called via this code:

require("biomaRt")
pig <- useMart("ensembl", dataset = "sscrofa_gene_ensembl")

However, it seems that they also use HGNC symbols for pigs.

Alternatively, you could also use the pig annotations from Bioconductor to do the conversion.

Let me know if you any need help with that.

Best wishes, Daniel

dbdimitrov commented 2 years ago

PS, it is important to note that CellChat requires some additional information about mediators which are not available for species other than mouse or human. So, if you use other species, you shouldn't call CellChat via LIANA.

i.e. you need to specify the methods that you want to use, e.g.:

liana_wrap(seurat_object, method = c("squidpy", "sca", "natmi", "connectome", "logfc"))

I hope this helps.

Goultard59 commented 2 years ago

It's works very well, thanks for your time.

Best Regards, Adrien.