PepNet
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lkytal
The state of the art Deep CNN neural network for de novo sequencing of tandem mass spectra
Hi, i was trying to follow the tutorial, but i couldn't find the python script "evaluation.py" `python evaluation.py --mgf example.mgf --novorst example_prediction.tsv` Can you tell me where i can download...
Hi, Our dataset have lots of modifications which are important, is it possible to modify the model a bit, such that we can train PepNet from scratch by ourselves to...
Hi, I came across a paper related to PepNet. I want to integrate it in my de novo sequencing pipeline, but I am wondering if it is possible to get...
I'm currently considering including PepNet in [Galaxy](https://galaxyproject.org/), i.e. to add a Galaxy tool. For this, a conda package for Pepnet would be required. I could work on both (actually I...
After running the following command: `python denovo.py --input example.mgf --model model.h5 --output example_prediction.tsv` I get this error lib/python3.7/site-packages/keras/engine/input_spec.py", line 200, in assert_input_compatibility raise ValueError(f'Layer "{layer_name}" expects {len(input_spec)} input(s),' V**alueError: Layer...
It works fine when denovo from the provided model, (model.h5). When training our own model, there is an error Train mode runs successfully, however, if we used the trained model...
Hello, Thank you for sharing this great tool! I am currently working with denovo DIA data and encountered some confusion. From my understanding, the input for the DeepNovo-DIA model consists...
Since TensorFlow Addons (TFA) has ended development, setting up PepNet with newer versions of Python has become very challenging. Could you please provide a version that replaces Addons with another...
Hi, I had this error in one of my PepNet jobs: PyteomicsError('No mass data for residue: ' + e.args[0]) pyteomics.auxiliary.structures.PyteomicsError: Pyteomics error, message: 'No mass data for residue: Z' I...
