How to download Transcriptome data for differential gene expression analysis from National cancer institute GDC data portal

Question

[bookorg]

I want to download the transcriptome data of a particular cancer for DEG analysis.But i am unable to do that.When I get into the server i cannot found the download and desired file.So I am eagerly asked for help,so that I can able to download that easily.

[GenoMax]

Not sure what exactly you are looking to do but you can also find analyzed data at https://www.cbioportal.org/

[bookorg]

Thanks.But i want to download gene expression data of breast cancer and wanted to analyse Differentially gene expression from that.

Answer 1

[Zhenyu Zhang]

Are you talking about you don't know how to use GDC repository https://portal.gdc.cancer.gov/repository? Or just you don't know which file type can be used for DEG?

Answer 2

[Sumit Paliwal]

You can look at the following resources: https://f1000research.com/articles/5-1542 https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/download_prepare.html