Answers.Body: <p>I personally find the GDC portal not very user-friendly. However, some of the data is available from other sources. For example, you can download TCGA-BRCA FPKMs and phenotypes from UCSC Xena here: <a href="https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)" rel="nofollow noreferrer">https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)</a></p>
  
  <p>All the sample info is already combined and the labels are the classic TCGA barcodes.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-02T11:12:43.390Z
Answers.Text: I would give a try with the R/Bioconductor package "TCGABiolinks" (https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html). The vignettes are quite helpful for various steps of data retrieval, including filtering based on user defined criteria.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-03T10:06:39.393Z
Answers.Text: http://gepia2.cancer-pku.cn/ try this
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-27T21:19:21.230Z
Answers.LastActivityDate: 2018-07-27T21:19:21.230Z
Answers.UserDisplayName: burger
Answers.Body: <p>These data are in Experiment Hub in Bioconductor</p>
  
  <pre><code>library(curatedTCGAData)
  brcaRNA &lt;- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-09T11:42:46.103Z
Answers.Text: If you could expand your answer to explain how this helps to link data from the samples to each sample it would make a great answer
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-08T21:56:07.987Z
Answers.LastActivityDate: 2019-01-08T21:56:07.987Z
Answers.UserDisplayName: Aedin
Body: <p>I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (<a href="https://portal.gdc.cancer.gov/repository" rel="nofollow noreferrer">https://portal.gdc.cancer.gov/repository</a>) to classify breast cancer subtypes (luminal A, luminal B, HER2-like, basal-like).</p>
  
  <p>However, since I don't know the portal, I'm having problems in associate the EXP data and the label.</p>
  
  <p>I could get the label either by using the old TCGA-barcode and use a dictionary I already have from an article (but I don't know how to get the barcode from the portal / API) or by using clinical data (but I don't know how to find metadata that link the EXP and the clinical data).</p>
  
  <p>Is there anyone more used to the portal who could help me?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-25T13:24:10.130Z
Comments.Text: Your question doesn't give enough details for even someone familiar with this portal to try and help, I think. Do you have an example of a dataset you want to interrogate, and how it is deficient in the details you require?
Comments.UserDisplayName: sjcockell
Tags: <public-databases><cancer><data-download><data-retrieval>
Title: GDC data portal cancer subtype
ThreadText: # GDC data portal cancer subtype
  
  (Asked by: username_0 on 2018-07-25)
  
  I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (<https://portal.gdc.cancer.gov/repository>) to classify breast cancer subtypes (luminal A, luminal B, HER2-like, basal-like).
  
  However, since I don't know the portal, I'm having problems in associate the EXP data and the label.
  
  I could get the label either by using the old TCGA-barcode and use a dictionary I already have from an article (but I don't know how to get the barcode from the portal / API) or by using clinical data (but I don't know how to find metadata that link the EXP and the clinical data).
  
  Is there anyone more used to the portal who could help me?
  
  **Tags:** public-databases, cancer, data-download, data-retrieval
  
  > **Comments:**
  > **username_1**: Your question doesn't give enough details for even someone familiar with this portal to try and help, I think. Do you have an example of a dataset you want to interrogate, and how it is deficient in the details you require?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2018-07-27. Score: 1
  
  I personally find the GDC portal not very user-friendly. However, some of the data is available from other sources. For example, you can download TCGA-BRCA FPKMs and phenotypes from UCSC Xena here: <https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)>
  
  All the sample info is already combined and the labels are the classic TCGA barcodes.
  
  > **Comments:**
  > **username_3**: I would give a try with the R/Bioconductor package "TCGABiolinks" (https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html). The vignettes are quite helpful for various steps of data retrieval, including filtering based on user defined criteria.  
  > **username_4**: http://gepia2.cancer-pku.cn/ try this  
  
  ---
  
  ### Answer by username_5 on 2019-01-08. Score: 1
  
  These data are in Experiment Hub in Bioconductor
  
  ```
  library(curatedTCGAData)
  brcaRNA <- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
  
  ```
  
  > **Comments:**
  > **username_6**: If you could expand your answer to explain how this helps to link data from the samples to each sample it would make a great answer  
  
  ---
  
  