TCGAbiolinks
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BioinformaticsFMRP
TCGAbiolinks
Hello, I have been having a huge struggle with the TCGAvisualize_starburst command. > starburst_lowvsint
Dear all, I have downloaded HTSeq-Counts harmonized data for Lung Adenocarcinoma. Raw counts look like this: ``` TCGA-44-7671-01A-11R-2066-07 TCGA-49-6744-11A-01R-1858-07 TCGA-05-4432-01A-01R-1206-07 ENSG00000207629 0 0 0 ENSG00000207644 0 0 0 ENSG00000207699 0...
Hi, thanks for developing such a awesome tool! I download ”gene level copy number“ using TCGAbiolinks, and I supposed there are five values: -2(del),-1(loss),0(diploid),1(gain),2(amp). But when I download the data.type...
I run this # Enrichment Analysis EA # Gene Ontology (GO) and Pathway enrichment by DEGs list Genelist.PRAD
Hello people, I'm new here, maybe my question is a little silly! Excuse. I am unable to find a function to search for the overexpressed DEGs of interest. #Performed the...
I'm running a DEG example (essentially like the vignettes) and I get the following error code when trying to run TCGAvisualize_EAbarplot: ``` > TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP), + GOBPTab = ansEA$ResBP,...
Hello there your package seems amazing however i am not able to install it on both MacOS and linux. I have an issue with 2 packages openssl, GenomeInfoDbData on MAC...
I tried to install the package in R studio it gave me this error message BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Installing package(s) 'BiocVersion' Warning: unable to...
Hi @tiagochst and All, I am new with TCGA data and interested to plot 3D-Tsne using methylation data from TCGA. Below is my snippet for 2D Tsne plot. Can you...
False: Test failed:'GDCquery can filter by data.category' * There is no "GDCquery" function
