TCGA data application

[xiachenrui]

Hi, @andrewsong90, @ajv012

It is a impressive work!

I would like to request access to the pre-extracted patch embeddings and gene expression data for all TCGA cohorts. I understand that the size of the data may pose challenges for sharing, but I can provide my FTP server for direct transfer.

Best.

[ajv012]

Thanks for your interest in our work. We provide UNI patch embeddings and associated RNA profiles as .pt files for TCGA-BRCA at this LINK. Please let us know if you have any trouble accessing this.

[xiachenrui]

Thanks for replying, I want to know if it is possible to share pre-extracted patch embeddings and gene expression data for ALL TCGA cohorts.

Best!

[ajv012]

At this point, we are not able to share it for the entire TCGA cohort.

[MichealgodJordan]

Thanks for your interest in our work. We provide UNI patch embeddings and associated RNA profiles as .pt files for TCGA-BRCA at this LINK. Please let us know if you have any trouble accessing this.

Could you please share the method you obtain the RNA .pt files? I saw another collaborator share the preprocessing method to obtain a CSV file, but I have no idea about how to extract its feature into .pt file in your way. Could you please provide code or examples? Thanks.