maximilianh/cellBrowser

gene expression and proteins together

mxposed opened this issue · 4 comments

mxposed commented

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 commented

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 commented
mxposed commented

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 commented