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### Description of the bug
Im processing a dataset using proteomicsLFQ and it fails when it found empty list of peptides in one of the idXMLs.
```
TOPPBase.cpp(1605): Value of string option 'kee…
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We need to build a tool to load all GEO GDS datasets (GDS datasets contain curated metadata) It should support incremental update.
Useful resources:
- http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess…
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### Description of feature
Apologies if I'm directing my query to the wrong place, but I was wondering whether there is any plan to allow the newest version of DIA-NN (1.9.2) in the DIA pipeline as I…
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Hi all,
I made a pull request with three exemplary annotations for MSI data to start a discussion: https://github.com/bigbio/proteomics-metadata-standard/pull/450
Here are some thoughts about t…
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@jpfeuffer sometimes the pipeline fails in the id part because of the peak-peaking step by the ThermoRawFileParser. Would be great to "restart" the pipeline, same parameters but with the openms peak p…
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Hi All,In the LC-MS Analysis of Isoaspartylated Peptides part of the PXD006112 project, the experiment uses a mixture of 12 peptides to conduct the experiment, so Organization、 Organization part, etc.…
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Thank you so much for creating this package; it's been revolutionary for spicing up the standard Seurat figures! As a novice bioinformatician, I'm afraid I've run into a small issue that I hope I coul…
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### Project short name: LungOrganoidsTCR
### Primary Wrangler:
Arsenios
### Secondary Wrangler:
Wei
### Associated files
* Google Drive: [folder](https://drive.google.com/drive/folders/10Bmm…
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Hi everyone,
I generated an updated LFQbenchmark dataset, similar to the one from Navarro et al. (https://pubmed.ncbi.nlm.nih.gov/27701404/). I was wondering how I could best annotate the mixtures…
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Hi, Thanks for providing such a fantastic tool.
We are going to add DIANN's information to OLS @ypriverol, please confirm whether the following information is correct:
- Name of the main score at th…