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rnabioco / djvdj

An R package to analyze single-cell V(D)J data
https://rnabioco.github.io/djvdj
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wrapper for export to ucsc cell browser #19

Open raysinensis opened 3 years ago

raysinensis commented 3 years ago

Would this be of some interest?

sheridar commented 3 years ago

@raysinensis having a wrapper that creates a cellbrowser that includes VDJ data would definitely be useful. I know @kriemo has written some code to do this, but not sure if it's structured as a single function.

A separate but related thing I was thinking about is that it might also be useful to write an AWS wrapper in bash that automates the process for setting up the password protected buckets we use for the browsers

kriemo commented 3 years ago

It's not a single function yet, but it wouldn't be hard to port the code from some of my projects.

I have code that generates another assay in the seurat object to store the clonotype data as a binary matrix (e.g): https://github.com/rnabioco/Rincon_scVDJseq/blob/7e5742dfc4f168dcc909b91e3f9355ae9f397c3c/results/qc.Rmd#L864

The wrapper that I use for generating cellbrowsers is in the scbp package, which allows you to add additional assays to the cellbrowser (via concatenating the matrices).

Here's an example: https://github.com/rnabioco/Rincon_scVDJseq/blob/7e5742dfc4f168dcc909b91e3f9355ae9f397c3c/results/cb.Rmd#L97

sheridar commented 3 years ago

@kriemo this seems like a nice way to store additional vdj data in the object. Maybe we should just incorporate your version of the import function