Answers.Body: <p>There isn't <strong>a</strong> R/Bioconductor person or view, so there isn't a preferred way to access TCGA. Use what suits you. </p>
  
  <p>Bioconductor is build by contributors which are encourage to not overlap in their contributions. Usually the packages have different options/features even if they allow to access to the same data.  </p>
  
  <p>In this case, the TCGAbiolinks package is specifically for TCGA dataset while GenomicDataCommons is for "access the NIH / NCI Genomic Data Commons RESTful service". So the functionality they bring to R and Bioconductor is different.</p>
  
  <p>The fact that one project is finishing doesn't mean that the data or the packages build around that project are obsolete. Some functionality different between them is the functions to harmonize and prepare (<code>GDCprepare</code>) data from the TCGAbiolink package, or see a boxplot correlation and AAIC plot to define outliers <code>TCGAanalyze_Preprocessing</code>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-19T22:43:18.910Z
Answers.Text: I understand that there is not a R/BioC person, but it seems that the TCGA project is coming to a close in 2017. On the other hand the NCI GDC is just starting and will include/already includes the TCGA data, hence my question... Is it really true that they bring different functionality? Because it seems the GenomicDataCommons package will include the same (or more) of the TCGAbiolinks functionality.
Answers.UserDisplayName: Ramiro Magno
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-20T07:00:12.037Z
Answers.Text: @plant See the updates in the answer
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-19T20:25:22.940Z
Answers.LastActivityDate: 2017-09-20T06:59:49.197Z
Answers.LastEditDate: 2017-09-20T06:59:49.197Z
Answers.UserDisplayName: llrs
Body: <p>It seems there are two packages providing access to TCGA data these days:</p>
  
  <ul>
  <li><a href="https://www.bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html" rel="nofollow noreferrer">TCGAbiolinks (older)</a></li>
  <li><a href="https://bioconductor.org/packages/release/bioc/html/GenomicDataCommons.html" rel="nofollow noreferrer">GenomicDataCommons (newer)</a></li>
  </ul>
  
  <p>Will <em>GenomicDataCommons</em> supersede <em>TCGAbiolinks</em>? Is there anything that I might miss if I decide to use only <em>GenomicDataCommons</em>?</p>
  
Tags: <r><bioconductor>
Title: What is the R/Bioconductor preferred way of accessing TCGA data?
ThreadText: # What is the R/Bioconductor preferred way of accessing TCGA data?
  
  (Asked by: username_0 on 2017-09-19)
  
  It seems there are two packages providing access to TCGA data these days:
  
  * [TCGAbiolinks (older)](https://www.bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html)
  * [GenomicDataCommons (newer)](https://bioconductor.org/packages/release/bioc/html/GenomicDataCommons.html)
  
  Will *GenomicDataCommons* supersede *TCGAbiolinks*? Is there anything that I might miss if I decide to use only *GenomicDataCommons*?
  
  **Tags:** r, bioconductor
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-09-19. Score: 1 | Accepted answer
  
  There isn't **a** R/Bioconductor person or view, so there isn't a preferred way to access TCGA. Use what suits you.
  
  Bioconductor is build by contributors which are encourage to not overlap in their contributions. Usually the packages have different options/features even if they allow to access to the same data.
  
  In this case, the TCGAbiolinks package is specifically for TCGA dataset while GenomicDataCommons is for "access the NIH / NCI Genomic Data Commons RESTful service". So the functionality they bring to R and Bioconductor is different.
  
  The fact that one project is finishing doesn't mean that the data or the packages build around that project are obsolete. Some functionality different between them is the functions to harmonize and prepare (`GDCprepare`) data from the TCGAbiolink package, or see a boxplot correlation and AAIC plot to define outliers `TCGAanalyze_Preprocessing`.
  
  > **Comments:**
  > **username_0**: I understand that there is not a R/BioC person, but it seems that the TCGA project is coming to a close in 2017. On the other hand the NCI GDC is just starting and will include/already includes the TCGA data, hence my question... Is it really true that they bring different functionality? Because it seems the GenomicDataCommons package will include the same (or more) of the TCGAbiolinks functionality.  
  > **username_1**: @plant See the updates in the answer  
  
  ---
  
  