Saket Choudhary

It is difficult to answer this question without a bit more context. If there are strong batch effets when analyzing both the datasets (no integration), you would need integration.

> Question 1. If I should do SCTransform() each of 6 datasets individually (or within each CD39+ or CD39- dataset?) (given high sample-effect https://github.com/satijalab/seurat/issues/2826 https://github.com/satijalab/seurat/issues/1580), how can I account for...

Hi @w-julie, this does appear to be a memory issue. How many cells do you have in your dataset and how much RAM does the system have?

Closing due to inactivity.

Thanks, I can confirm that it is currently broken. For now I could recommend dumping the metadata in a tsv and then using the `sra_url` field to download: ```bash $...

Thanks for reporting this and for the patch. I will fix this in the next release.

This is pretty straightforward, all you need is a mako template.[1]. I did it for Biojs.Sequence.js [2] One advantage I have had using Galaxy is to define what part of...

Would it make sense to push such templates in the main `biojs` repo. We could maybe have a separate branch for this if not the `master`?

Probably. Since this requires playing around with Galaxy's API, I will have to take a look.

It should be possible. https://wiki.galaxyproject.org/Learn/API