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27 Open 193 Closed
27 Open 193 Closed
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Issues list

Remove depthcharge MGF prefix bug workaround enhancement New feature or request
#387 opened Oct 4, 2024 by Lilferrit Depthcharge v0.4
Use full file path in the MztabWriter run map instead of just the file name. bug Something isn't working enhancement New feature or request
#386 opened Oct 4, 2024 by Lilferrit Depthcharge v0.4
Use lightning.pytorch.loggers.TensorBoardLogger for tensorboard logging. enhancement New feature or request
#382 opened Sep 18, 2024 by Lilferrit
Switch to geometric mean for peptide scores enhancement New feature or request
#381 opened Sep 18, 2024 by wsnoble
ReadTheDocs needs to be updated with new functionalities documentation Improvements or additions to documentation
#377 opened Sep 17, 2024 by bittremieux
@Lilferrit
Implement early stopping / validation patience interval. enhancement New feature or request
#375 opened Sep 6, 2024 by Lilferrit
1
ValueError upon unexpected scan title format bug Something isn't working
#354 opened Jul 7, 2024 by MNTsnowman
1
7
Make Casanovo model compatible with torch.compile enhancement New feature or request
#347 opened Jun 25, 2024 by Lilferrit
Use Fourier embeddings enhancement New feature or request
#345 opened Jun 25, 2024 by wsnoble
Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo question Further information is requested
#337 opened May 18, 2024 by CCranney Depthcharge v0.4
1
3
Make Casanovo produce Skyline compatible output enhancement New feature or request
#330 opened May 14, 2024 by wsnoble
@justin-a-sanders
Export casanovo to torchscript/onnx enhancement New feature or request
#328 opened May 11, 2024 by LLautenbacher
1
Add rotary embeddings enhancement New feature or request
#321 opened Apr 17, 2024 by wsnoble
Implement bidirectional decoding enhancement New feature or request
#320 opened Mar 27, 2024 by wsnoble
1
add additional inputs to encoder and decoder enhancement New feature or request
#318 opened Mar 27, 2024 by wsnoble
1
where are the models trained with my own data saved? question Further information is requested
#291 opened Feb 11, 2024 by DIGEdige Casanovo v5.0.0
@Lilferrit
2
Rank of updates array (1) must be greater than or equal to inner-most dimension of indices array (29) bug Something isn't working macos
#285 opened Jan 29, 2024 by wsnoble
1
KeyError: '$' bug Something isn't working macos
#284 opened Jan 25, 2024 by patrick-willems
18
Casanovo does not check for repeated m/z values in spectra
#272 opened Dec 19, 2023 by cfmelend Depthcharge v0.4
2
Add min_peaks config option enhancement New feature or request good first issue Good for newcomers
#264 opened Nov 10, 2023 by wsnoble Depthcharge v0.4
1
Add the option to turn off the precursor m/z filter entirely enhancement New feature or request
#247 opened Sep 22, 2023 by melihyilmaz Casanovo v5.0.0
1
Add reflected spectrum encoder enhancement New feature or request
#214 opened Jul 19, 2023 by wsnoble
2
Fix error message "TypeError: Can't implicitly convert non-string objects to strings" bug Something isn't working
#207 opened Jul 10, 2023 by wsnoble Depthcharge v0.4
3
Add brackets and hyphens to PTMs enhancement New feature or request
#201 opened Jun 28, 2023 by wsnoble Depthcharge v0.4
5
Track scan numbers in MGF files enhancement New feature or request
#142 opened Mar 2, 2023 by wsnoble
ProTip! What’s not been updated in a month: updated:<2024-09-06.