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Hi,
I was trying to run Inspire using ms2pip instead of Prosit, but I ran into an issue that I'm not sure how to solve. The software is supposed to generate the file ms2pipInput.preprec to start ms…
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Could you add a table to the documentation that better summarises the available models? Something analogous to the MS2PIP model table: [https://github.com/compomics/ms2pip?tab=readme-ov-file#specializ…
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I'm getting an uncaught exception when trying to use ms2rescore.feature_generators.ms2pip.DeepLCFeatureGenerator. The error happens when there are not enough peptides in psm_list for the calibration s…
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I thought this idea was large enough where it should be it's own issue even though it's part of #1124 .
@acesnik wants some HTML reports and I think a lot of users really want some way to easily/gr…
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### Description of the bug
I have problems using MHCquant with multiple variable modifications.
The whole pipeline works when not specifying any modifciations.
With multiple modifcations, the pip…
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Hi,
Thank you for developing MS2PIP.
[diann_001.txt](https://github.com/compomics/ms2pip/files/15249813/diann_001.txt)
I have a pre-digested (trypsin) FASTA file and I want to create an in sil…
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The description of hackathons could be more homogeneous. Even though the writing may closely derive from an abstract written by a different author/organizer, it should have a common section each time:…
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This feature request came up in https://github.com/nf-core/mhcquant/issues/317
Currently, the xgboost models are always downloaded to `$HOME/.ms2pip`. In some cases that could lead to permission is…
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I'm getting a mysterious pickling error when trying to use ms2rescore.feature_generators.ms2pip.MS2PIPFeatureGenerator. The error seems to be caused by having [UNIMOD:nn] variable mods in the ProForma…
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Hi,
I imported the library predicted by sofware named MS²PIP into DIA-NN, and ended up with an empty matrix report.
However, when I use the library-free mode (DIA-NN) alone, the results are norma…