Integration of different species datasets

[giorgiatosoni]

Thank you for this amazing tool!

• Would it be possible to add a feature to convert gene names in the corresponding orthologs, for integration across different species?
• Would it be possible to add 'Features Mito/Ribo Functions' for macaca mulatta?

[samuel-marsh]

Thanks so much!!
In terms of conversion across orthologs that is something I’ve thought about but don’t have simple solution I like yet (I just use biomaRt currently).

I will add macaca mulatta this morning. I’ll ping here when active in dev branch.

Best,
Sam

[samuel-marsh]

Hi @giorgiatosoni macaca mulatta is now live in both the Seurat and LIGER mito functions. Dev branch (v0.7.0.0015). Let me know if you run into any issues.

See:

Add_Mito_Ribo_Seurat(list_species_names = T)

  Mouse_Options Human_Options Marmoset_Options Zebrafish_Options Rat_Options Drosophila_Options Macaque_Options
1         Mouse         Human         Marmoset         Zebrafish         Rat         Drosophila         Macaque
2         mouse         human         marmoset         zebrafish         rat         drosophila         macaque
3            Ms            Hu               CJ                DR          RN                 DM          Rhesus
4            ms            hu               Cj                Dr          Rn                 Dm          macaca
5            Mm            Hs               cj                dr          rn                 dm        mmulatta
6            mm            hs             <NA>              <NA>        <NA>               <NA>            <NA>

I'm going to close issue for now but know that gene conversion is something that I'm thinking about and if/when I figure out a way I like to do it then I'll ping you here.

Best!
Sam

[giorgiatosoni]

Hi,

I still don't see the macaque options..

Best,

Giorgia

[samuel-marsh]

Hi Giorgia,

Did you install off of the develop branch? What is result of:

packageVersion("scCustomize")

Best,
Sam

[samuel-marsh]

Also sorry realized I got confused about your first question on gene conversion and was thinking about ensembl to symbol conversion. For conversion between species I recommend using the orthogene package. Available either from BioConductor or GitHub:
https://bioconductor.org/packages/release/bioc/html/orthogene.html
https://github.com/neurogenomics/orthogene

Best,
Sam

[giorgiatosoni]

Hi Giorgia,

Did you install off of the develop branch? What is result of:

packageVersion("scCustomize")

Best, Sam

packageVersion("scCustomize")
[1] ‘0.7.0’

[samuel-marsh]

oh yes need to install off the develop branch until I move this onto a new release.

In new R session run:

devtools::install_github("samuel-marsh/scCustomize", ref = "develop")

Best,
Sam

[giorgiatosoni]

Thanks a lot!!

Best,

Giorgia

[samuel-marsh]

No problem!! :)