-
```
$ time R CMD check TCGAbiolinks_2.8.2.tar.gz
real 31m8.456s
user 11m28.293s
sys 1m17.121s
```
Much of the time appears to be spent in examples and tests downloading data (I watch…
-
Hi,
I want to run some TCGA queries using TCGAbiolinks package inside my nextflow pipeline.
Is there a recommended dockefile to make use in this case?
I tried this but it didn't work. the TCG…
-
Hello,
I have TCGAbiolinks GUI installed on my server, here at FMRP/Ribeirão Preto. When I start the GUI, it appears with a gray layer over the interface, giving the impression of being inactivated. …
-
It crashes when I try to open it. There are also several problems when I try to install it. I am using TCGAbiolingsGUI version 1.5.2 and TCGAbiolinks 2.7.6
edit: When it crashed this message appear…
-
From a cancer microarray dataset analysis, i have identified a small gene signature, which i would like to validate further through RNA-Seq data and TCGAbiolinks. However, i wondered for one further…
-
Hello
When I used TCGAbiolinks for downloading clinical data, I found a problem in XML clinical data.
In XML clinical data, There is a column that shows new_tumor_event_after_initial_treatment or …
-
I have downloaded SARC RNA-seq data by HTseq-Count workflow type through TCGAbiolinks. But I need SARC RNA-seq data based on Transcripts Per Million (TPM) value. Can TCGAbiolinks help me to download T…
-
Hi,
Thanks for TCGAbiolinks package, it is very useful. One thing i wonder, how i can get the information on platform for tcga samples, some cancers were sequenced on different platforms (such as G…
-
Hi,
I cannot select an IDAT folder (see attached image); it's just blank and no options to choose from. Same thing with "set working directory" under configuration. "Select file to download" under …
-
Hello.
Thank you for developing this amazing resource. I am having some problems with normalizing RNAseq data from TCGA. In brief, I am doing a "sanity check" using breast cancer data subdivided into…