TCGAbiolinks
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BioinformaticsFMRP
TCGAbiolinks
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...
Hello, I'm getting the following errors while trying to compile the clinical XML files. The download finished successfully but the GDCprepare_clinic command fail. How can it be fixed? Thanks, Assaf...
**I was trying to access clinical data for the project CTSP-DLBCL1 without success. I suspect a bug.** GDCquery() was functional and resulted 37 hits: ```r query.1 sessionInfo() R version 4.3.2...
Hello, I am having an issue preparing mutation and proteomics data from the TCGA-READ and COAD projects. I have used this same method for gene expression data which worked fine...
[This line](https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/e78993d11ca7ea3259b4ba2fba94f22bd2b2d4c5/R/analyze.R#L864C5-L872C6) in the `analyze.R` code leads to the following error if you don't set metadata to FALSE and if your samples have different sample IDs: ```r Error in names(x)
I was trying to obtain STAR gene expression data from multiple datasets including TCGA, TARGET, and CPTAC. Some errors happened when preparing some projects, and they are mainly related to...
Hi, I tried both ``` if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("TCGAbiolinks") ``` and ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") ``` But it reports: cannot open URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES' Warning:...
Hello, I have encontered an error using GDCprepare with gene expression data from BEATAML1.0-COHORT, while trying to add clinical information to samples: Error in `dplyr::bind_cols()`: ! Can't recycle `..1` (size...
Hi, Thanks for a very useful package. Great work:) I have just tried (using `v2.32.0`) to download the allele-specific copy number segments from TCGA, as exemplified in the code examples...
