TCGAbiolinks
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BioinformaticsFMRP
TCGAbiolinks
GDCdownload(query_col_wxs, directory = "TCGA_DATA_DL") Downloading data for project TCGA-COAD GDCdownload will download 457 files. A total of 82.8324 MB Downloading as: Sat_Feb_17_21_15_58_2024.tar.gz Downloading: 83 MB The same error occurred in...
hi, **1.** When I follow your tutorial Case study n. 1: Pan Cancer downstream analysis BRCA, error raised in: ``` dataSurv % as.numeric ` with `mRNAselected_values % dplyr::filter(rownames(dataCancer) == mRNAselected)...
getProjectSummary() is not available in version 2.22.4 although the function is present in the help documentation `> getProjectSummary() Error in getProjectSummary() : could not find function "getProjectSummary"`
Hi, I am able to successfully use TCGAanalyze_SurvivalKM to generate Kaplan-Meier curves, however, I cannot move where the legend is placed. Is there a way to do this? Best, Sam
Hello there, I'm trying to download the clinical data from GDC TCGA, but when I run the following code: ``` GDCquery_clinic(project = "TCGA-TGCT") ``` it gave me this error: ```...
Hi, the Debian paackaged TCGAbiolinks is tested on different release architectures. While the test suite is passing on some architectures there is a failure which occures on [armel](https://ci.debian.net/packages/r/r-bioc-tcgabiolinks/testing/armel/41009180/), [armhf]( https://ci.debian.net/packages/r/r-bioc-tcgabiolinks/testing/armhf/41009181)...
Good afternoon, I am having issues with GDCPrepare with the CPTAC-3 dataset for scRNA-seq data. I have successfully downloaded the data with ``` #Query the data query.exp
I did ```r library(TCGAbiolinks) query_cnv In addition: Warning message: > In rep(no, length.out = len) : 'x' is NULL so the result will be NULL Debugging GDCprepare found out the...
Dear Colleagues, I'm currently following the TCGA Workflow published on https://www.bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#Methods as is. Everything works fine until I try to merge exp_gbm and exp_lgg summarizedExperiment objects via the code: `exp_gbm_lgg
