Hello, I am trying to download the data used in a specific paper to benchmark the performance of their model. The paper I am referring to is "Classification of Cancer Types Using Graph Convolutional Neural Networks" (https://www.frontiersin.org/articles/10.3389/fphy.2020.00203/full). In the Data preparation section of the paper, it is mentioned that they downloaded 11,071 data samples in December 2018. I want to download the data for that specific period, but I don't know how to do it. I am not very familiar with using Github, so I would appreciate it if you could guide me on how to download the data from either the GDC portal or Github (https://github.com/RicardoRamirez2020/GCN_Cancer). Thank you very much.
•
written
by
wyt1995 •
1 answer
You should ask the authors for uuids of these file.
If they don't have it, you can check which data release is around Dec 2018, and using GDC API to find data of that particular data release. This depends on your familiarity of GDC APIs. I am not sure if other packages like GDC or TCGAbiolinks support such query.
Log in to answer this question.
-
filter genes for differential gene expression
written by bleven •
-
How can validate hub genes or significant factors using area under the ROC curve (AUC)?
written by wyt1995 •
-
What do I download from the GDC Data portal for a methylation analysis? Files or Cases?
written by ananta.kapoor •
-
mismatch sample number TCGA ovary cancer between recount and GDC portal
written by BrunoGiotti
-
GDC portal data download
written by a01039012387 •
-
Accessing controlled cancer data
written by Gene_MMP8
-
TCGA COAD and READ annotations missing from GDC commons?
written by ckr123 •
-
Where to get somatic mutations from WGS data?!
written by dankoc •
-
GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
written by dsull
-
Getting subtypes of cancer from TCGA
written by noorpratap.singh
