gene expression and proteins together

[mxposed]

Hi,

I wonder what configuration and object looked like for these objects? https://cells.ucsc.edu/?ds=multimodal-pbmc+sct We have a gene expression + CITE-seq data for several objects, and we'd like to use cellbrowser for that, but I couldn't find a recipe in the documentation.

Thank you cc @karolinasenkow

[matthewspeir]

Hi, @mxposed.

We also now have a cellbrowser-confs repo, and so I've added the *conf files and a small README for this dataset: https://github.com/ucscGenomeBrowser/cellbrowser-confs/tree/main/multimodal-pbmc. Let me know if that's helpful at all.

To summarize though: data was in h5seurat format, exported the matrices for ADT + RNA expression separately, then configured a cellbrowser.conf for each dataset to point to a different matrix but to shared meta + coords files.

I think this dataset was also an ADT + RNA expression dataset: https://engraftable-hsc.cells.ucsc.edu. For that one, the submitter provided us a matrix for both assays and then we configured them in a similar way: https://github.com/ucscGenomeBrowser/cellbrowser-confs/tree/main/engraftable-hsc.

[maximilianh]

I may be wrong, but isn't expression + ADT in the same matrix for a cite-seq experiment? If so, we should be able to handle this without any changes, I hope?

On Wed, Jun 15, 2022 at 1:23 AM Matt Speir @.***> wrote:

Hi, @mxposed https://github.com/mxposed.

We also now have a cellbrowser-confs https://github.com/ucscGenomeBrowser/cellbrowser-confs repo, and so I've added the *conf files and a small README for this dataset: https://github.com/ucscGenomeBrowser/cellbrowser-confs/tree/main/multimodal-pbmc. Let me know if that's helpful at all.

To summarize though: data was in h5seurat https://mojaveazure.github.io/seurat-disk/index.html format, exported the matrices for ADT + RNA expression separately, then configured a cellbrowser.conf for each dataset to point to a different matrix but to shared meta + coords files.

I think this dataset was also an ADT + RNA expression dataset: https://engraftable-hsc.cells.ucsc.edu. For that one, the submitter provided us a matrix for both assays and then we configured them in a similar way: https://github.com/ucscGenomeBrowser/cellbrowser-confs/tree/main/engraftable-hsc .

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/247#issuecomment-1155801838, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TONXIKWUHW4S72SENTVPEIAHANCNFSM5YZBOD5Q . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[mxposed]

Thank you @matthewspeir for the examples!

@maximilianh We can put ADT together with RNA in the same matrix (currently in a separate), but I guess the main question is about overlapping gene/protein names. I suspect cellbrowser won't handle that, so I should just name the proteins differently, and all names should be unique, right?

[maximilianh]

Yes just make them unique. Add a prefix or suffix.

Hmm… we’ll need some way in the UI to make this obvious … any idea ?

On Wed 15 Jun 2022 at 20:11, Nikolay Markov @.***> wrote:

Thank you @matthewspeir https://github.com/matthewspeir for the examples!

@maximilianh https://github.com/maximilianh We can put ADT together with RNA in the same matrix (currently in a separate), but I guess the main question is about overlapping gene/protein names. I suspect cellbrowser won't handle that, so I should just name the proteins differently, and all names should be unique, right?

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/247#issuecomment-1156780559, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TKNL732ZYYNZN6AOCDVPIMDTANCNFSM5YZBOD5Q . You are receiving this because you were mentioned.Message ID: @.***>