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This is a case where the SwaggerParser from 1.0.36 works fine but the conversion to the OpenAPI with 2.0.1 fails. Clearly the dates are in an unexpected format but I expect specs that parse in Swagger…
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Moreover, if I understand correctly, it's literally the same thing as Lyman and Zuckerman cluster population analysis, with the exception that there they do it as a function of block size instead of j…
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I noticed there are two reference options. one is hs and another is dm. Are they for human and mouse?
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In imzspectrum interface add a deconvolution method that returns a list of masses.
Parameters could specify the max charge possible (useful for ms2 where precursor charges are known), confidence leve…
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@mangiapasta and @ajschult - you guys got a great draft going for the specific observables section. I have some questions/comments that hopefully you could address in the next few days:
- I think …
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Fixes that need to be solved:
- [x] `data_protein_quantification.txt` and `data_protein_quantification_Zscores.txt`: replace the headers to `Composite.Element.REF` instead of `Hugo_Symbol`.
- [x] `d…
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To circumvent this problem, remove the protein_quantification files from these studies.
- [x] `coadread_tcga`: Both `data_protein_quantification` and `data_protein_quantification_Zscores` have dupl…
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Hello
I am trying to upload brca_tcga.tar.gz to the latest version of cbioportal. During the validation, files meta_protein_quantification.txt and meta_protein_quantification_Zscores.txt produce err…
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Hi,
I tried the analysis as in https://github.com/chapmanb/bcbio-nextgen/issues/2162 with also transcript_assembler activated.
I used this yaml file
```
# Template for RNA-seq using Illu…