User: tiagochst

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tiagochst90
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Brazil
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2 weeks, 2 days ago
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2 years, 11 months ago
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Posts by tiagochst

<prev • 24 results • page 1 of 3 • next >
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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 20 days ago by tiagochst90
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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 20 days ago by tiagochst90
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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 9 months ago by tiagochst90
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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 9 months ago by tiagochst90
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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 13 months ago by tiagochst90
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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 13 months ago by tiagochst90
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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 14 months ago by tiagochst90
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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 15 months ago by tiagochst90
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Answer: A: Problem in downloading data via TCGAbiolinks
... Hi Sab,   Yes, is this because of the recent changes in TCGA. I rewrote the code do work with GDC. It is already in the github repository, but I still need to update bioconductor repository, which should be done until next week. This gist has the last version of the code: https://gist.github.com ...
written 16 months ago by tiagochst90
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Answer: A: Problems running TCGAbiolinks
... Hi, The problem is related to the maintenance of TCGA data portal.  As we are not sure it will comeback, we are rewriting the code to make TCGAbiolinks use GDC database instead the old TCGA data portal. There should be an update in the coming weeks in Bioconductor repository, but if you would lik ...
written 16 months ago by tiagochst90

Latest awards to tiagochst

Scholar 19 months ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks
Scholar 22 months ago, created an answer that has been accepted. For A: Data download via TCGAbiolinks

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