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Hi Tiago,
thank you for your incredibly helpful package, I used it a lot recently and it works great. (I am using
Bioconductor 3.10, BiocManager 1.30.10, R 3.6.3).
For the NCICCR-DLBCL proje…
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#### What data file(s) does this issue pertain to?
We currently only have gene expected counts and not raw counts in the data releases.
#### What release are you using?
v12
#### Put you…
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According to your paper, the total number of TCGA-NSCLC slides is 993 and you used 4-fold cross-validation, so each slide is classified once in hold-out sets after the cross-validation.
By checking …
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Hi @briannapagan & team,
I have been invited by ESA to deliver a presentation on our GeoZarr working group's activities during the upcoming CEOS WGISS #54 meeting on April 19th, 2023. CEOS is respo…
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I understand there is CPTAC clinical metadata in ISB-CGC that matches our images. @G-White-ISB can you please investigate how it is organized, how it is versioned, how it can be linked with images, so…
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## Context
**Issue type** (bug report or feature request):
**Operating system** Ubuntu 18.04.5 LTSD
**Platform** Intel x86-64
**OpenSlide version**: 3.4.1
**Slide format** SVS
## Details
I…
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Variant validation is incorrectly failing on Bulk Publish for certain models. This is likely related to:
* https://github.com/nci-hcmi-catalog/portal/commit/e71f2a1e81b871ab986b6ce9e428e71f013021cd
…
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#### What data file(s) does this issue pertain to?
```
tcga-gene-counts-rsem-expected_count-collapsed.rds
tcga-gene-expression-rsem-tpm-collapsed.rds
```
#### What release are you using?
…
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It seems this is due to recent changes in GDC Data Portal, which affect `TCGAbiolinks` as well (https://support.bioconductor.org/p/9143118/#9143119).
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How to select Omics data sets on TCGA?How to preprocess data sets?