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i am using this issue to provide info on the data i use when benchmarking wsinfer in qupath.
image: TCGA-3C-AALI-01Z-00-DX1.F6E9A5DF-D8FB-45CF-B4BD-C6B76294C291.svs ([link to image for download](ht…
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Hi RMolania! Thanks for the very useful approach. I want to use RUV-III with PRPS for non-TCGA RNA-seq data, but I don't know how to process the non-TCGA RNA-seq data to use RUV-III with PRPS. Would y…
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The following link show a protein length of 699 for gene BRCA1 but PTM track has dots over 699
https://www.cbioportal.org/results/mutations?cancer_study_list=ov_tcga_pub&cancer_study_id=ov_tcga_pub&ge…
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There are parts of the GDCtools code which either make reference to TCGA (in the comments) or directly assume TCGA context (in the code). Both of these are No-Nos, and need to be scrubbed from the co…
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Fix the issues that the CHECK command produces:
```
==> devtools::check()
Updating imogene documentation
Warning: Version of roxygen2 last used with this package is 7.1.1. You only have versi…
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How did you figure out patients' survival information (time to event) from TCGA RNA-seq data? There seems to be no feature indicating survival or censorship.
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Hi @dami82 ,
I need to have the most relevant signature per TCGA samples. Please comment on my take below.
```
# Retrieve exposures (results)
tcga.exp tcga.sign[,1:3]
TCGA-02-0003-01 T…
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Hi Martin, @mtmorgan
I am unable to see the error message from `gsutil cp -m`:
It is somehow cut off.
```r
gsutil_cp(assayfiles, rpath)
Error: 'gsutil -m cp gs://firecloud-tcga-open-acce…
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Following curl responds empty. Which is what [explains](https://beta.cbioportal.org/patient?studyId=coadread_tcga_pan_can_atlas_2018&caseId=TCGA-F5-6864)
curl 'https://beta.cbioportal.org/api/struc…
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这是我最终理想化的想要得到的数据形式。
对TCGA，nonPCAWG，PCAWG/ICGC这三个数据来源的数据，各种癌症类型的cox回…