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better edge case errors for proteogenomic data
1. sample with only 1 analyte in data `!all(names(data) %in% names(probeAssay))`
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Galaxy server : usegalaxy.eu
Tool version : Galaxy Version 0.1.1
(1) History which contains execution of SearchGUI+Peptide Shaker with the **comprehensive** database (reference+variants+indel+alt sp…
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@husensofteng and @yafeng I think PEFF http://www.psidev.info/peff will become soon the standard database for proteogenomics. We should evaluate if we want to generate also databases using PEFF annota…
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Hello, I am running the Galaxy Proteogenomics workflow through my command line and i seem to be stuck at how to execute the query_tabular tool in command line, can you please share with me a simplifie…
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Currently, I filter out transcripts lacking strand. In these cases, we could use information from the gene model to look for the best match, use that strandedness if it exists, and filter the strandle…
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Greetings
I would like to know if answers to the questions from the jupyter notebooks will be made available here in GitHub
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Hi @timosachsenberg and @all :
We have been using OpenMS and proteomicsLFQ to perform LFQ-proteogenomics analysis of public proteomics data. We have used and stringent FDR at the peptide level to …
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Hi,
From today's spatial meeting, it sounds like there's a need to clarify the two types of `.mat` files in Visium and Visium Spatial Proteogenomics (Visium-SPG) processing pipelines, to avoid this…
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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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### Description of feature
@daichengxin #contributors
With the support of SAGE by quantms, we have opened the possibility to support a quantms open-search workflow. I recommend the following ste…