Bo

Example for training a BERT model from scratch using new data without using pre-trained weights

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Hi, The library looks great. I'm trying to use BERT for biological sequence tasks so I cannot use the pre-trained models with language data. Could you provide an example to...

Hi, Is it possible to support the DT (https://rstudio.github.io/DT/) for table visualization in nozzle framework? Best regards! Bo

Is that possible to add a parameter in ggpie to control removing whitespace around pie chart? ```R df

It looks the version number from the release page doesn't match that showing from the command line.  $ percolator --help Percolator version 3.06.0, Build Date May 11 2022 12:43:04...

User provided spectral library

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For a user provided spectral library, how does DIA-NN select fragment ions in the library for peptide detection?

Decoys in spectral library

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How does DIA-NN recognize decoys in a spectral library? Is it based on the column "Decoy" as shown below in the library? | Decoy | |---| | No | |...

PDV - Mac

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The files in a folder doesn't show when the GUI is opened by double-clicking: 

The peptide sequence is gone from the export panel for some cases:  

Exporting report doesn't work as shown below:  ``` Exception in thread "Export" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1 at PDVGUI.gui.PDVMainClass.getSpectrum(PDVMainClass.java:3912) at PDVGUI.utils.ExportReports$1.run(ExportReports.java:152) ```

The m/z values for neutral loss are not correct: