yanailab / pancancer Goto Github PK

Dear Yanai Lab,

I can not download the Rdata stored in the Dropbox (https://www.dropbox.com/sh/jh4s57kgbb0rnxe/AABoMK466cGc1OKsOuFN10wca?dl=0).

Would you provide the OneDrive download link for us?

Thank you very much!!

Pillar

Hi,

It's a great work you've done and congratulate.

I notice in the annotation, you used singleR described as:

Part 2: The SingleR package v.1.4.1 (ref. [19](https://www.nature.com/articles/s41588-022-01141-9#ref-CR19)) was used with the Human Primary Cell Atlas database

And I find the reference is not a scRNA dataset, and it's a chip data of human primary cell.
Can you explain why you use chip data instead of scRNA data as reference, because I have never seen people used a non-scRNA data for singleR. And does it make a good sense?
Besides, I can't find the expression data in the reference article, could you serve it for me?
An expression atlas of human primary cells: inference of gene function from coexpression networks | BMC Genomics | Full Text

Thanks a lot, and waiting for you reply.

Hi! I found your finding very interesting. I wonder if you can provide modules.RData for modules. I was trying to go over the whole process to get the cell state values.
Thank you!
Peiyao

Dear authors,
Hi!
There is a small problem puzzling me that I can not find R package named ‘MSigDB’ in CRAN or Bioconductor. The packages similar to 'MSigDB’ are msigdbr in CRAN or msigdb in Biocondutor. However, none of them meet the demand of codes, especially in function FindMSigDB. Could you please check this package whether it is available or not?
Thanks!
@daliabarkley

Hi @daliabarkley, would you be able to provide the robjs you created for this analysis? Thanks

Hi, please could you point me in the correct direction to find the cell types assigned to the breast scRNA data used in this paper? Thanks!