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**Describe the bug**
Hello,
I'm trying to generate a spectral library from Thermo DDA runs. I'm running FragPipe in headless mode in Linux with a workflow copied from the GUI to include spectral l…
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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/odisce/phenomis
Confirm the following by editing …
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Dear Gabriel,
Do you see a reason why not using the dream function on proteomics abundance data, or particular issues? Input to dream() here would be a simple matrix of normalized intensities rathe…
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🐞 **Describe the bug:**
Dear all,
I've been working on a research project consisting out of a microbiome data set and several metabolomics data sets. In this data set, I only have …
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Whenever I've implemented some change regarding sample sheets, I've tested the results with a bunch of different ISAtabs and some configurations of data in a dev iRODS server. Alas, this is not suffic…
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- Describe the issue or question:
I am trying to run an open search for peptide modifications on a mzML file using this workflow https://fragpipe.nesvilab.org/docs/tutorial_open.html
I am able to ru…
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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/Vitek-Lab/MSstatsShiny
Confirm the following by e…
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### Description of the bug
@daichengxin when only one search engine is used in the analysis the mzTab is reporting a q-value rather than a PEP (posterior error probability).
One example run here:…
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Dear authors/developers,
I am attempting to perform differential expression analysis with multiple methods. All of the methods work without any issue, except for DESeq2 which produces the following…
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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:
…