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Issues list

Tuning MS2 by low-quality fragment matches on all DIA PSMs at apex_rt resulted in low-quality MS2 prediction
#124 opened Dec 31, 2023 by jalew188 updated Jan 12, 2024
1
Library translate tsv: IndexError: index 4 is out of bounds for axis 1 with size 4
#142 opened Feb 6, 2024 by J-Burgess updated Feb 15, 2024
1
Missing the documentation on how to use the GUI to train a model for in-silico prediction
#149 opened Mar 19, 2024 by michaelsteidel86 updated Mar 19, 2024
3
Supported fragmentlosstype?
#153 opened Apr 15, 2024 by hxxhust163 updated Apr 17, 2024
4
ModelManager.predict_all() modifies dataframe in place
#163 opened May 7, 2024 by GeorgWa updated May 21, 2024
@jalew188
1
Copy transformer code from huggingface due to too many breaking changes
#178 opened Jun 25, 2024 by jalew188 updated Jun 25, 2024
@jalew188
Tutorial: immunopeptidomics
#183 opened Jun 28, 2024 by jalew188 updated Jul 2, 2024
@wahlema
peptdeep bug on linux - destination is read-only
#177 opened Jun 17, 2024 by timheymann updated Jul 12, 2024
@GeorgWa
A problem about the GUI page
#185 opened Jul 16, 2024 by jalew188 updated Jul 16, 2024
Tutorial: speclib
#187 opened Jul 17, 2024 by jalew188 updated Aug 8, 2024
@jalew188
FutureWarning: torch.load changed weights_only=False to weights_only=True
#195 opened Aug 12, 2024 by jalew188 updated Aug 12, 2024
The epoch parameter in scheduler.step() was not necessary and is being deprecated where possible
#194 opened Aug 10, 2024 by jalew188 updated Aug 12, 2024
@mo-sameh
1
Custom LR scheduler not supported
#191 opened Aug 1, 2024 by ErikHartman updated Aug 12, 2024
1
Can you issue a GUI guide
#198 opened Aug 16, 2024 by yanzhou-boy updated Aug 16, 2024
Finetune a pretrained model on a new dataset without using mode_x to optimize performance for the new target.
#199 opened Aug 18, 2024 by shamimshahcheraghi updated Aug 19, 2024
1
About zipfile.BadZipFile: File is not a zipfile problem
#200 opened Aug 19, 2024 by yanzhou-boy updated Aug 19, 2024
1
Requirement to replace our pretrained RT model
#204 opened Aug 23, 2024 by jalew188 updated Aug 23, 2024
Transfer learning to refine predicted library
#145 opened Feb 22, 2024 by snsipe updated Aug 28, 2024
3
IndexError: positional indexers are out-of-bounds,May kind people be blessed with life-long peace.
#207 opened Aug 28, 2024 by yanzhou-boy updated Aug 28, 2024
KeyError: 'Modified.Sequence'
#203 opened Aug 23, 2024 by yanzhou-boy updated Sep 10, 2024
1
Why is "rescore" is not available as a task_choice
#212 opened Oct 8, 2024 by mhamaneh updated Oct 9, 2024
1
@C/N-term mods do not create in silico modified peptides bug Something isn't working
#214 opened Nov 6, 2024 by S-Watanabe0123 updated Nov 7, 2024
Translation for speclib.tsv fails while handling modifications
#218 opened Nov 28, 2024 by JuliaS92 updated Nov 28, 2024
Mod site for C-term modifications question Further information is requested
#209 opened Sep 24, 2024 by mo-sameh updated Feb 14, 2025
1
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