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I think it would be a good idea to include the `Proteomics Data Acquisition Method` to explain the type of experiment, this term is in the `NCI Thesaurus OBO Edition` ontology and the terms are:
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### Description of the bug
Following advice from @jpfeuffer, I'm making the switch from the "nf-core/proteomicslfq" workflow to "nf-core/quantms" (dev version in both cases). I'm surprised to find th…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/RforMassSpectrometry/MsExperiment/
Confirm the f…
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Hi,
I've noticed that setting the subset-max-train argument on Percolator has a very large impact on PSM yield even when the number of PSMs in the dataset is much smaller than the value set in the …
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Hi,
I want to experiment with the search function of RawTools. I tried this command on linux, but it seems no search is started. There is also no error message and I did not find anything about thi…
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Hi there
Very cool paper! I'm curious about the details of how you learned the pattern of missingness in the initial peptides-by-samples matrices. I'm referring to this step of the implementation out…
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Dear Bioconductor team,
Please find below the GitHub link to the "phenomis" package that we would like to submit to Bioconductor.
The package provides methods for the post-processing (quality co…
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Dear Bioconductor team,
Please find below the GitHub link to the "phenomis" package that we would like to submit to Bioconductor.
The package provides methods for the post-processing (quality co…
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Hello all,
I tried using Metaboverse to combine Proteomics and Metabolomics data of mouse livers. I think I formatted the data correctly, but when I start building a network, it is stuck at 0% perman…
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Hello,
I am working with label-free quantitative (LFQ) proteomics and am interested in adapting your R package workflow for use with results obtained from ISOQuant (an opensource package for Top…