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I am trying to run histoqc on selected files in a dataset (TCGA Breast) using
python -m histoqc -c /workspace/histoqc_config.ini -n 3 /workspace/tcga_path_histoqc.tsv
where tcga_path_histoqc.ts…
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Run this against the TCGA genie database, you'll see some kind of "not serializable" error in java logs. Note that the server DOES respond, so this error may have to do with trying (and failing) to …
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Thank you for your work. May I ask how did you obtain these csv files? The data I downloaded from TCGA seems to be different, and I couldn't find some labels' data in the csv files.
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Hi,
I have been unable to connect to the GDC server for a few hours now.
My query:
```
query sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running un…
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Hi Tiago,
my previously working script to download RNAseq expression data from GDC fails with the error message "`tar: unrecognized archive format`". I tried downloading with `method` set to `client…
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Hi,
I'm trying to run callTumorOnly, but I got the following error:
Starting parallel pool (parpool) using the 'local' profile ...
connected to 16 workers.
message =
finished processing chromo…
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Let's put datasets here. In order to avoid confusion, the dataset refers to curated data from the database which we can use in ml and AI models. Database refers to Clinvar where they have raw data onl…
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The released WSI-VQA dataset only has 7139 VQA pairs. Why the size of the dataset is not the same as the reported in the paper?
Btw, I have checked the slide names in [TCGA ](https://portal.gdc.canc…
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Would it be possible to concatenate multiple VCF files into a single Zarr store, preserving sample information, with sgkit?
As an example, I got two files, vcf1, where sample1 is stored, and vcf2, …