TCGA学习1--下载level3 level4数据

1、使用firehose_get   下载level3 level4数据

https://confluence.broadinstitute.org/display/GDAC/Download

example:

• firehose_get analyses latest
  Retrieves: every result, for every disease cohort, in the latest GDAC Firehose run

• firehose_get -tasks mutsig gistic  analyses latest brca ucec
  Retrieves: only Gistic and MutSig results for breast and uterine cancer

• firehose_get -tasks mut analyses latest prad
  Retrieves: all results which have "mut" in their name, such as MutSig, Mutation_Assessor, and any correlations to mutation data

2、R包

https://github.com/mariodeng/FirebrowseR

devtools::install_github("mariodeng/FirebrowseR")

3、GDC网站

比较麻烦

4、cbioportal

一般我只看网页版

5、其他等等

先学学firehose