How to select checkbox with specific names on web page (the TCGA data)

Question

[Xinsen Xu]

Hi, I want to download the RNA-seq data from the TCGA website. After I built the data matrix on the TCGA website, there are hundreds of the checkboxes. However, I only want to download the ones with the specific name rsem.genes.normalized_results, because I only needed the normalized data. It is too time-consuming to click one by one. Could anyone help to show me some more simple way to do it? Thank you so much!

Answer 1

[karl.stamm]

How to select checkboxes would be some kind of Javascript or client programming question. We don't need to solve this obscure problem, when the root issue was how to download a lot of TCGA normalized data. See this program instead to easily download what you need without using their website.

http://www.compgenome.org/TCGA-Assembler/

[Xinsen Xu]

Hi Karl, Thanks so much. I've downloaded the TCGA-Assembler, however, after I installed the Rtools31 and downloaded the httr version 0.5.0., and tried to type install.packages("httr_0.5.tar.gz", type="source", repos=NULL)

it turned out that

"ERROR: dependency 'jsonlite' is not available for package 'httr'
* removing 'C:/Program Files/R/R-3.2.0/library/httr'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.2.0\library" "httr_0.5.tar.gz"' had status 1
Warning in install.packages :
  installation of package 'httr_0.5.tar.gz' had non-zero exit status"

Could you help to tell me how to solve this problem? Thank you so much!

[karl.stamm]

That's a computer problem, maybe your IT admin can help install the packages. It's a common enough issue with R packages. Read the error message, "dependency jsonlite is not available"

So first you'll have to install.packages("jsonlite") and it should download from CRAN automatically.

I tried it now, httr also wants a package called "R6" which was installed automatically when completing

install.packages("httr")

You don't have to specify repos=NULL, and it will download for you.