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### Description of feature
After parsing the SDRF, we should check if the OpenMS experimental design is also up to the OpenMS standard.
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- [x] parse OBO
- [x] construct DAG
- [x] use [HumanSamples.sdrf.xlsx](http://fantom.gsc.riken.jp/5/datafiles/phase2.0/basic/HumanSamples2.0.sdrf.xlsx) to filter out primary cells, tissues, cell lines…
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### Description of feature
Inmunopeptidomics is one of the use cases that quantms can try to handle in the same way that we are planning to handle Proteogenomics. For Inmunopeptidomics we will need t…
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e.g. in SDRF we usually have the tolerances, their units, and the instrument name.
BUT: The search engines have restrictions.
They usually take only high_res vs low_res for some additional setting…
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test issues
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It would be nice to have links to the most relevant repositories and resources related to `sdrf-pipelines` in the `README.md`. e.g. to the https://github.com/bigbio/proteomics-metadata-standard repo.
…
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This does not only apply to this repo, but rather to all our pipelines:
Do we want to collect results of only one default dataset, or also of other datasets?
For the default datasets: let's add so…
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### Description of the bug
I get the following error when running quant.ms using an sdrf.tsv file:
Error in setnames(x, value) :
Can't assign 4 names to a 0 column data.table
Calls: OpenM…
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It seems that somehow MANIFESTS are not getting the cell_to_library lines written even though studies do have cell_to_library.txt files within the bundle:
```
(miniconda3)[host results]$ ls -l */*…
pcm32 updated
2 years ago