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From the publication worldwide shows that BRAF V600E is most common point mutation, but recently I worked on the TCGA dataset, all V600E were converted to V640E which is so different from the data in …
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I am trying to analyze the TCGA –LIHC dataset for DEGs but when I get to the data normalization, it says that it is not found
`>dataNorm
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library(SummarizedExperiment)
library(TCGAbiolinks)
library(dplyr)
query.exp
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I am new to `TCGAbiolinks` and learning to download TCGA clinical data using:
```R
clinical
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I'm trying to run GDCquery_Maf function
My code which i took from one of the tutorial
```
library(TCGAbiolinks)
library(maftools)
packageVersion("TCGAbiolinks")
[1] ‘2.22.4’
```
The e…
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Hello,
I'm trying to use TCGAbiolinks for Methylation study on prostate cancer. I have an error saying "found some probes with NA for all samples in your data, please either remove/or replace them". …
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When I try to download anything else than Count type files I get this type of error. I am talking about HNSC files with clinical data box checked.
Error
Error while preparing the files
Error in…
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Hi,
I ran this command 2 weeks ago, it ran perfectly.
query = GDCquery(project = 'TCGA-LUAD',
data.category = 'Transcriptome Profiling',
data.type = 'Gene Ex…
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I've been trying to use TCGAbiolinks to download the CPTAC data but I've run into a problem with the methylation data. I have been able to download the data but I can't integrate it together using GDC…
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When running PAMES::get_purity(beta) it seems to require normal samples beta values and the AUC-file. Is it possible to run it using only beta-values from the tumor sample?
Best,