TCGA下载神器--TCGAbiolinks

http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#gdcquery:_searching_tcga_open-access_data

 

举例：

Working with TCGAbiolinks package

Antonio Colaprico, Tiago Chedraoui Silva, Luciano Garofano, Catharina Olsen, Davide Garolini, Claudia Cava, Isabella Castiglioni, Thais Sarraf Sabedot, Tathiane Maistro Malta, Stefano Pagnotta, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr

2017-12-06

Updates

Recently the TCGA data has been moved from the DCC server to The National Cancer Institute (NCI) Genomic Data Commons (GDC) Data Portal In this version of the package, we rewrote all the functions that were acessing the old TCGA server to GDC.

The GDC, which receives, processes, harmonizes, and distributes clinical, biospecimen, and genomic data from multiple cancer research programs, has data from the following programs:

• The Cancer Genome Atlas (TCGA)
• Therapeutically Applicable Research to Generate Effective Treatments (TARGET)
• the Cancer Genome Characterization Initiative (CGCI)

The big change is that the GDC data is harmonized against GRCh38. However, not all data has been harmonized yet. The old TCGA data can be acessed through GDC legacy Archive, in which the majority of data can be found.

More information about the project can be found in GDC FAQS

The functions TCGAquery, TCGAdownload, TCGAPrepare, TCGAquery_maf, TCGAquery_clinical, were replaced by GDCquery, GDCdownload, GDCprepare, GDCquery_maf, GDCquery_clinical.

And it can acess both the GDC and GDC Legacy Archive.

Note: Not all the examples in this vignette were updated.

Introduction

Motivation: The Cancer Genome Atlas (TCGA) provides us with an enormous collection of data sets, not only spanning a lar