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**Describe the bug**
The conversion from a network to a pytorch geometric object is corrupted:
- The edge features is given as a list of string instead of a list of lists:
- When we have edges asso…
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Hi Vadim,
I encounter a problem while using DIA-NN for my experiments. I created a spectral library from 13 fasta files which contains around 40 000 proteins (called LibA). When I run the raw data …
agdup updated
11 months ago
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Hi PDV community,
I was trying to visualize some .pepXML results and .mzXML files exported from PEAKS Studio 10.5.
However, I am receiving an error (attached image) that is preventing me to do a…
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# Title
Making sense of internal fragment ions
# Abstract
Peptide identification from fragment mass spectra uses only part of the contained information. Here, internal fragment ions, i.e. pep…
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my command:
java -jar /share/liuqi/ganyuli/proteome/software/PDV-1.7.4/PDV-1.7.4.jar \
-r combined \
-rt 5 \
-s . \
-st 1 \
-i tab2.txt \
-k s \
-o output \
-a 0.5 \
-c 5 \
-pw 1 \
-fw 800…
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Between 8am and 4pm PT, on July 4th, the ontology build started to fail, bringing down or blocking multiple pipelines. Looking at the PRs in that window, I suspect the changes happened earlier, but to…
kltm updated
2 months ago
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My raw files were searched with DIA-NN 1.8.1 and the output table "report.pg_matrix.tsv" was used for further analysis. I was confused with the two columns "Protein.Group" and "Protein.Ids". The colu…
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Hi, Vadim
I recently want to test DIA-NN function of phosphosite localization. I downloaded the raw MS data which included 166 synthetic phosphopeptides spiked in yeast lysate and the spectral libr…
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Ville Koskinen is working on mzIdentML 1.2 export from Mascot and reports this issue:
we're looking at what changes are needed to export mzIdentML 1.2 from Mascot Server. One problem we've encounte…
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Might be good to implement a flag from command line to enable turning on and off (we can set default to on) this behaviour. In case at some circumstances that people don't want to care this, For exam…