Noble-Lab casanovo issues

Noble-Lab / casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

https://casanovo.readthedocs.io

Apache License 2.0

90 stars 31 forks source link

issues

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Designate a filename for the "best" model

#351 wsnoble opened 21 hours ago
3
Migration to depthcharge v0.4.8

#350 andradesalazar opened 1 day ago
0
Download weight file from URL

#349 Lilferrit opened 5 days ago
1
Fix documentation of --output and updated output settings.

#348 Lilferrit opened 6 days ago
1
Make Casanovo model compatible with torch.compile

#347 Lilferrit opened 1 week ago
0
Add mzTab validator to github actions

#346 wsnoble closed 1 week ago
1
Use Fourier embeddings

#345 wsnoble opened 1 week ago
0
Restrict NumPy to pre-2.0

#344 bittremieux closed 1 week ago
1
Enhanced Sequencing Run Logging

#343 Lilferrit opened 1 week ago
11
CLI documentation page generation

#342 Lilferrit opened 1 week ago
0
mzTab validation fix

#341 Lilferrit closed 1 week ago
1
313 save final model

#340 Lilferrit closed 4 days ago
8
Numpy release 2.0.0 breaks depthcharge dependency

#339 Lilferrit closed 1 week ago
2
Is there a way to know which spectras are ITMS instead of FTMS?

#338 Heisenburger2020 closed 3 weeks ago
3
Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo

#337 CCranney opened 1 month ago
3
Compatible 9-species data reference

#334 bittremieux closed 1 month ago
1
9-Species Benchmark Set: Data Preprocessing Step?

#333 CCranney closed 1 month ago
5
Update CHANGELOG.md

#332 melihyilmaz closed 1 month ago
1
Prepare release v4.2.0

#331 bittremieux closed 1 month ago
1
Make Casanovo produce Skyline compatible output

#330 wsnoble opened 1 month ago
0
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

#329 dadadalizi146 closed 1 month ago
3
Export casanovo to torchscript/onnx

#328 LLautenbacher opened 1 month ago
1
Don't test on macOS versions with MPS

#327 bittremieux closed 1 month ago
1
WARNING: Skipped spectra with invalid precursor info

#326 lutfia95 closed 1 month ago
1
Add Casanovo-DB Functionality

#325 VarunAnanth2003 opened 2 months ago
10
More information about the train/val/test split

#324 andradesalazar closed 2 months ago
2
Automate mzTab validation

#323 wsnoble opened 2 months ago
7
mzTab validation

#322 wsnoble closed 1 week ago
0
Add rotary embeddings

#321 wsnoble opened 2 months ago
0
Implement bidirectional decoding

#320 wsnoble opened 3 months ago
1
Add contrastive loss term

#319 wsnoble opened 3 months ago
0
add additional inputs to encoder and decoder

#318 wsnoble opened 3 months ago
1
Supported file formats documentation

#317 bittremieux closed 3 months ago
1
Allow csv to handle all newlines

#316 mobiusklein closed 3 months ago
3
What is the criteria of saving the top k models in Casanovo version 4?

#315 irleader closed 3 months ago
1
how to train casanovo v4 on huge dataset like massive-kb from scratch?

#314 irleader closed 3 months ago
3
Save final model

#313 wsnoble closed 21 hours ago
1
No Models Saved, No Validation Loss Reported

#312 grahamdelafield closed 3 months ago
3
Using HDF5 file as train/val dataset leads to index out of bound error

#311 cfmelend closed 3 months ago
9
Add FAQ about MGF index tracking

#310 melihyilmaz closed 3 months ago
3
Question about tracking spectra from MGF files in output

#309 JannikSchneider12 closed 4 months ago
1
Exclude some PTMs for prediction?

#308 JannikSchneider12 closed 4 months ago
2
Version 4 is more accurate but much slower than version 3?

#307 irleader closed 3 months ago
4
Don't crash when multiple beams have identical peptide scores

#306 bittremieux closed 4 months ago
1
[v3.5.0 ValueError] in the denovo mode of prediction with pretrained massive-kb model

#305 irleader closed 4 months ago
1
Add FAQ entry about antibody sequencing

#304 wsnoble closed 4 months ago
1
Add 9-species model weights link to FAQ

#303 melihyilmaz closed 4 months ago
1
Casanovo v4.1.0: RuntimeError about NVIDIA driver even CPU mode

#302 progistar closed 4 months ago
2
Run unit tests on macOS with M1 support

#301 bittremieux closed 1 month ago
3
Rename max_iters to cosine_schedule_period_iters

#300 bittremieux closed 4 months ago
2