User: eshelden

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eshelden20
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1 month, 2 weeks ago
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e*******@vetmed.wsu.edu

Posts by eshelden

<prev • 6 results • page 1 of 1 • next >
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Answer: A: update TCGAbiolinks to version 3.6 and GDCquery doesn't work
... Try installing the most recent version from github. https://github.com/BioinformaticsFMRP/TCGAbiolinks ...
written 14 days ago by eshelden20
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Answer: A: TCGABiolinks::GDCquery() suddenly sending back unknown error
... I also "suddenly" encountered an error in GDCquery today. However, installing the version currently available on github solved my problem. You may find that version at the following link: https://github.com/BioinformaticsFMRP/TCGAbiolinks ...
written 19 days ago by eshelden20
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Answer: A: TCGAbiolinks Download ERROR
... I got the same error using a query that worked a few weeks ago using "TCGA-BRCA". There is a version of TCGABiolinks on github that appears to have solved the issue. You can find it here: https://github.com/BioinformaticsFMRP/TCGAbiolinks On my platform, installation required: install.packages("d ...
written 19 days ago by eshelden20
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Answer: A: Constructing a Summarised Experiment object
... I've used TCGAbiolinks to create a SummarizedExperiment from the data available at the GDC. It might also be useful for working with files you have already downloaded, but I have not tried that. ...
written 5 weeks ago by eshelden20
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What's the correct way to normalize HTseq files with TCGAbiolinks
... I am learning to process data from the Genomic Data Commons using TCGAbiolinks in R, but I have run into an issue normalizing the data using the routines built into TCGAbiolinks. In brief, I checked the results of the analysis by looking at breast cancer data that was divided into estrogen receptor ...
rnaseq normalization R bioconductor written 6 weeks ago by eshelden20
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Answer: A: TCGAvisualize_EAbarplot Function Issue
... R did this to me too. Turns out, it created the graph in a PDF file in the current folder. ...
written 6 weeks ago by eshelden20

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