User: tiagochst

gravatar for tiagochst
tiagochst150
Reputation:
150
Status:
Trusted
Location:
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Last seen:
2 weeks, 6 days ago
Joined:
3 years ago
Email:
t********@usp.br

Posts by tiagochst

<prev • 70 results • page 1 of 7 • next >
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Comment: C: Error in print.header("GDCquery: Searching in GDC database", "section") :could n
... Hi, this is an internal function, but it should be visible. Please, could you sent the listSamples and the package version (packageVersion("TCGAbiolinks"))? ​       ...
written 23 days ago by tiagochst150
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Comment: C: TCGAbiolinksGUI is not stable on windows 7.
... We added a function to normalized DNA methylation idats that uses that missing package (although we might change to sesame in the future). You should be able to install the missing dependency with: source("https://bioconductor.org/biocLite.R") biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg1 ...
written 6 weeks ago by tiagochst150
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Comment: C: TCGAbiolinksGUI is not stable on windows 7.
... Please, could you try the GitHub version? You can install with: ​devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI") ...
written 6 weeks ago by tiagochst150
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Comment: C: TCGA biolinks - Samples with multiple profiles
... The way TCGAbiolinks was structured it is not possible to do the query requested. You would need to go through a series of single manifests, filtering and merging.I'm not sure which WXS data you wanted, or which RNA-seq but the code below can be easily modified. https://gist.github.com/tiagochst/83 ...
written 7 weeks ago by tiagochst150
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Comment: C: TCGAbiolinks OutPuts (5% Losing Information)
... Hello, To create a summarizedExperiemnt object in TCGAbiolinks we have to map genes, probes etc into genomic coordinates. We decide to map those to the most updated ENSEMBL patched version. For humans those versions are GRCh38.p12 (hg38) and GRCh19.p13 (hg19). Since the version we are using, some o ...
written 10 weeks ago by tiagochst150
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Answer: C: TCGAbiolinks gives error when parsing a txt file (instead of expected xml)
... Hello I fixed the documentation yesterday. It seems the parsed TXT were added to the same group as the XML files. You need to add file.type = "xml" as filter.  query <- GDCquery(project = 'TCGA-KIRC', data.category = "Clinical",file.type = "xml") ...
written 4 months ago by tiagochst150
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Comment: C: GDCquery fail in some project , for example: TCGA-COAD mRNA
... GDC api moved to another path. Some versions of libcurl seems not to be able to redirect. We updated the link to api. It should be fixed now. Could you please update the package from github with devtools::install_github("BioinformaticsFMRP/TCGAbiolinks") Best regards, Tiago ...
written 4 months ago by tiagochst150
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Comment: C: GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-REA
... Hello,   I just made an update I believe will solve the problem. Could you update the package from github with devtools::install_github("BioinformaticsFMRP/TCGAbiolinks") and test it, please? ...
written 4 months ago by tiagochst150
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Comment: C: DESeq2 differential analysis - log2FC doubt
... Thank you very much for the help! ...
written 4 months ago by tiagochst150
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Comment: C: DESeq2 differential analysis - log2FC doubt
... But that's weird because I did not get that. And the rownames and colnames were different.   > colnames(all_cell_lines_ordered[,-c(1:7)],) [1] "IOSE11" "IOSE4" "FT246" "FT33" "EEC16" "EFO27" "GTFR230" "MCAS" "OAW42" "VOA1056" "CaOV3" "HEY" "UWB1_ ...
written 4 months ago by tiagochst150

Latest awards to tiagochst

Scholar 4 months ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 19 months ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 2.5 years ago, created an answer that has been accepted. For A: Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
Scholar 2.5 years ago, created an answer that has been accepted. For A: Getting a flat metadata table from the XML files in TCGA: is it feasible?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Multiple problems with TCGAbiolinks 2.2.6

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