TCGAWorkflow

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Multiple errors and unavailable packages when trying to install TCGAWorkflow

3

I'm doing a fresh install of R/RStudio. When I go to install `TCGAWorkflow`, I get several errors. Here is a summary of all the error lines when running `BiocManager::install("TCGAWorkflow")`: ```r...

leowill01

Firstly this improves some of the shortcomings of the jet scale (see [here](https://ai.googleblog.com/2019/08/turbo-improved-rainbow-colormap-for.html)). Secondly, this removes the need for the non-free `matlab` package.

jonasfreimuth

While applying the command- met.gbm.lgg

tmccse

Got Error in getFirehoseData function

1

Hello, I am trying to run code below: ``` # Download GISTIC results lastanalyzedate

luoyuan1984

i am working on TCGA database and want to prepare clinical data for analysis and normalization.i have data in csv format ,for TCGA biolinks preparation file can be in CEL...

HUSAIN23

GDCprepare-There are samples duplicated. We will not be able to prepare it

1

I met this error. it sames that i can download all the data but can not merge them. Error in GDCprepare(query = query.met.lusc, save = TRUE, save.filename = "luscDNAmet450k.rda", :...

cailiangliang765

Hello, I'm using the TCGAWorkflow package. My issue here is that I have an error that says that this package does not exist. I'm currently working with the 3.5.1 version...

IgnasiCI97

package ‘TCGAWorkflow’ is not available

2

> The downloaded source packages are in > ‘/common/tmp/RtmplmKhxH/downloaded_packages’ >Warning message: >package ‘TCGAWorkflow’ is not available (for R version 3.4.4) >The downloaded source packages are in > ‘/common/tmp/RtmplmKhxH/downloaded_packages’ >Warning message:...

RobertBakaric

GAIA aberrant region description

1

I followed the TCGAWorkflow to run GAIA using TCGA Malignant melanoma (SKCM) level 3 segment data. According to [GAIA load_cnv documentation](https://www.rdocumentation.org/packages/gaia/versions/2.16.0/topics/load_cnv), estimated copy number for segmented regions (kind of aberrations)...

PubuduSaneth

Please update the contents in Bioconductor Workflows section

1

Hi, I found the example code in the website is sometimes tricky to run (e.g. the code in **Visualizing multiple genomic alteration events section**, see below), what's more, in the...

mckf111