User: tiagochst

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tiagochst110
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110
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Location:
Brazil
Last seen:
11 months, 2 weeks ago
Joined:
4 years, 6 months ago
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Posts by tiagochst

<prev • 26 results • page 1 of 3 • next >
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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 11 months ago by tiagochst110
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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 13 months ago by tiagochst110
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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 19 months ago by tiagochst110
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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 19 months ago by tiagochst110
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Comment: C: TCGAbiolinks maf files RAS mutation rate not matching maf files from firehose
... Hi, Yes you can download MAF aligned to hg19, but it is not in the manual, I'm adding it. https://gist.github.com/tiagochst/03f5a11aa45d67940d65c8dd9bc90a70 Yes, the difference is really big!  From GDC Faqs Why might variants found in TCGA-generated MAFs be missing from the GDC open access MAF ...
written 2.3 years ago by tiagochst110
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Comment: C: TCGAbiolinks maf files RAS mutation rate not matching maf files from firehose
... One difference is GDCquery_Maf is accessing data aligned to hg38 while the one in firehose was aligned to hg19.   ...
written 2.3 years ago by tiagochst110
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Comment: C: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... Does the code below works? https://gist.github.com/tiagochst/6477e92006a09fedcc33f93e1e1dde21 ...
written 2.7 years ago by tiagochst110
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Comment: C: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... Could you send me the sessionInfo() from R ? Also, it this the last version of the package? ...
written 2.7 years ago by tiagochst110
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Answer: A: Error during GDCprepare
... This bug was in the biomart package. The server was down for maintenance. Now it is working. ...
written 2.8 years ago by tiagochst110
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Comment: C: Errors in TCGAbiolinks
... Hi,   They update GDC to version 2.0 and there was a change in the  API. I fixed it, it should be very soon in the bioconductor. Version 2.0.3 and 2.1.3.  The GDCquery error happend because their server was down for maintenance. Please, could you test with the github version for the moment. ...
written 2.8 years ago by tiagochst110

Latest awards to tiagochst

Scholar 3.2 years ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks
Scholar 3.4 years ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks

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