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Hi Tiago,
my previously working script to download RNAseq expression data from GDC fails with the error message "`tar: unrecognized archive format`". I tried downloading with `method` set to `client…
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Hello,
I get the following error when trying to download the harmonized TCGA data:
```
> GDCdownload(query)
Downloading data for project TCGA-BRCA
GDCdownload will download....
Starting to a…
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Instructors,
Please register your preferences here for using Amazon machine images (AMI) or for participant pre-installation of all software and data. I can take care of either if I know well enoug…
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Is it possible to perform differential expression analysis for each patient and to get the output logFC for each patient
Thanks.
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Hi there,
I am writing this issue because I have got this error with GDCprepare() used for proteomic (rppa platform) data :
> Error : $ operator is invalid for atomic vectors
I have noticed …
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Dear all,
We used your useful package to download the TCGA-SKCM dataset. However, we have inconsistencies according to follow-up times (days_to_last_follow_up) and times until death (days_to_death)…
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Hi there, I'm using this function, are you the authors? Where can I find the source code. I want to set default colours specifically for clinical annotations (as they are different for each oncoprint …
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Dear all,
I am trying to download the tissue slides for the TCGA-READ and TCGA-COAD project, but I am confronted with `/bin/tar: This does not look like a tar archive`. From my point of view it loo…
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I want to get gene-level copy number values for a couple of cancer types and I use
```r
library(TCGAbiolinks)
copyQuery
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Hello,
Thanks for this very helpful package. I have a question regarding accessing the subtype information associated with TCGA projects (in this example, specifically `COAD` but my question applie…