User: tiagochst

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tiagochst150
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Brazil
Last seen:
3 months ago
Joined:
4 years, 11 months ago
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Posts by tiagochst

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Matching TCGA Aliquot ID to UUID or Barcode
... Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils. From my code you would need to change the filter from barcode to aliquot ID. https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitter ...
written 3 months ago by tiagochst150
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Comment: C: Matching TCGA Aliquot ID to UUID or Barcode
... Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils. From my code you would need to change the filter from barcode to aliquot ID. https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitter ...
written 3 months ago by tiagochst150
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Comment: C: Matching TCGA Aliquot ID to UUID or Barcode
... Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils. From my code you would need to change the filter from barcode to aliquot ID. https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitter ...
written 3 months ago by tiagochst150
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Comment: C: Matching TCGA Aliquot ID to UUID or Barcode
... Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils. From my code you would need to change the filter from barcode to aliquot ID. https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitter ...
written 3 months ago by tiagochst150
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Comment: C: GDCprepare - error
... The package is outdated. We fixed that problem a month ago. Could you update the package, please with the following command: BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")? ...
written 3 months ago by tiagochst150
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Answer: A: TCGAbiolinks GDCprepare error
... Hello, This bug was solved two days ago, but I am not sure the fix is in Bioconductor yet. You update with the GitHub version with `BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")` Best regards, Tiago ...
written 4 months ago by tiagochst150
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Answer: C: Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks p
... That's a windows problem. Paths have a limit of 260 long path in windows. But it seems to be hackable in windows 10 (https://lifehacker.com/windows-10-allows-file-names-longer-than-260-characters-1785201032) ...
written 16 months ago by tiagochst150
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Comment: C: Error downloading TCGA miRNA expression data
... Hello,   There is no TARGET-OV in GDC. The code should be: query <- GDCquery(project = "TCGA-OV", data.category = "Transcriptome Profiling", data.type = "miRNA Expression Quantification") GDCdownload(query) counts <- GDCprepare(query) ...
written 18 months ago by tiagochst150
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Answer: A: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene
... You have the names inside the SummarizedExperiment object.   An example is in this gist: https://gist.github.com/tiagochst/fab346c19fa97d62a4bfb943024d1566   For hg38 the gene names are retrieved with values(data)$external_gene_name   For hg19  values(data)$gene_id   Where data is the s ...
written 2.0 years ago by tiagochst150
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Answer: A: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
...  Instead of the file you can pass the object. maf <- GDCquery_Maf("BRCA", pipelines = "muse", save.csv = TRUE) tcga_BRCA_maf <- read.maf(maf = maf, removeSilent = TRUE, useAll = FALSE) ...
written 2.0 years ago by tiagochst150

Latest awards to tiagochst

Scholar 16 months ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks
Scholar 3.5 years ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks
Scholar 3.8 years ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks

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