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wfondrie
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depthcharge
A deep learning toolkit for mass spectrometry
https://wfondrie.github.io/depthcharge/
Apache License 2.0
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Dataset cache design
#64
wang3702
opened
1 month ago
0
Scale to unit norm is wrong
#63
wfondrie
opened
1 month ago
0
Best practices for spectrum data loading
#62
bittremieux
opened
1 month ago
0
Skip spectra with invalid custom fields
#61
bittremieux
opened
1 month ago
1
Report number of batches in a spectrum dataset
#60
bittremieux
opened
1 month ago
3
Parser entry skipping based on custom fields
#59
bittremieux
opened
2 months ago
0
Error in reversing peptides with PeptideTokenizer.detokenize
#58
andradesalazar
opened
2 months ago
0
Error in analyte decoder when tokens is None
#57
andradesalazar
opened
2 months ago
1
SpectrumDataset: is a IterableDataset,How to use shuffle in Dataloader?
#56
cliang-huanglab
closed
2 months ago
1
Obtaining the retention time and ActivationType (e.g., HCD) from mgf files using Depthcharge
#55
junxia97
closed
2 months ago
1
Change `detokenize` behavior
#54
wfondrie
closed
4 months ago
1
Add stop/start tokens automatically to `AnnotatedSpectrumDataset` instances
#53
wfondrie
closed
4 months ago
1
Add support for unsigned masses in otherwise valid Proforma peptides.
#52
wfondrie
closed
4 months ago
1
Change `scan_id` dtype to string.
#51
wfondrie
closed
4 months ago
1
Remove `__len__()` for `IterableDataset` classes
#50
wfondrie
closed
4 months ago
1
Reflect `samples` argument in `SpectrumDataset` lengths
#49
wfondrie
closed
4 months ago
1
Quality of life fixes
#48
wfondrie
closed
4 months ago
1
Update the documentation page
#47
wfondrie
closed
4 months ago
1
Update Lance backend to use native PyTorch integration
#46
wfondrie
closed
5 months ago
1
Problem with AnnotatedSpectrumDataset and n_workers>0
#45
andradesalazar
closed
5 months ago
5
Example code to read .mgf file
#44
GuptaVishu2002
closed
4 months ago
6
Update API and add support for small molecules
#43
wfondrie
closed
6 months ago
3
Fixed Lance directory path bug in SpectrumDataset
#42
Alfred-N
closed
9 months ago
3
Add detail to invalid spectra warning parsers.py
#41
melihyilmaz
opened
9 months ago
1
Update Peptide Transformer API
#40
wfondrie
closed
6 months ago
0
Replace data backend and increase flexibility.
#39
wfondrie
closed
11 months ago
2
change tgt_mask to boolean
#38
justin-a-sanders
closed
1 year ago
3
Incorporate Wout's suggestions
#37
wfondrie
closed
1 year ago
1
Update changelog for release.
#36
wfondrie
closed
1 year ago
0
Update docs and readme.
#35
wfondrie
closed
1 year ago
0
Overhauled organization and interfaces
#34
wfondrie
closed
1 year ago
3
Fix version
#33
wfondrie
closed
1 year ago
1
Prepare for v0.2.1 release
#32
wfondrie
closed
1 year ago
1
Preprocess spectra before adding to index
#31
bittremieux
closed
1 year ago
5
Create target mask as bool
#30
bittremieux
closed
1 year ago
2
Log skipped
#29
bittremieux
closed
1 year ago
2
Fix the sinusoidal encoders
#28
wfondrie
closed
1 year ago
4
[bug] m/z encoding is incorrect
#27
wfondrie
closed
1 year ago
0
Use Ruff for linting
#26
wfondrie
closed
1 year ago
1
Remove tensorboard dependency
#25
wfondrie
closed
1 year ago
1
Why there is a replacement from "I" to "L" in peptide sequence during the tokenize function of _PeptideTransformer in transformer.py?
#24
liangzhendong123
closed
1 year ago
1
Fix calculation of m/z for charged peptides.
#23
mriffle
closed
1 year ago
2
Add option to dekonize peptide into AA list
#22
melihyilmaz
closed
1 year ago
6
Bump for first release
#21
wfondrie
closed
1 year ago
0
Don't crash on missing spectrum info
#20
bittremieux
closed
1 year ago
2
Add documentation site
#19
wfondrie
closed
2 years ago
0
Provide tokenization function
#18
bittremieux
closed
1 year ago
6
Specify whether the index is annotated
#17
bittremieux
closed
2 years ago
1
Existing index doesn't know whether it's annotated
#16
bittremieux
closed
2 years ago
2
Parse mzXML files
#15
bittremieux
closed
2 years ago
0
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