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compomics
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psm_utils
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
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`io.parquet`: Replace file hash-based tests with more specific tests
#106
RalfG
opened
1 week ago
0
Make pyopenms dependency optional
#105
RalfG
opened
1 week ago
0
Fix peptidoform modification offset and mass (fixes #100)
#104
RalfG
closed
1 week ago
1
Add I/O support for some DIA search engines
#103
rodvrees
closed
1 week ago
1
PSMList: Use np.fromiter when using a string as accessor (e.g. `psm_list["peptidoform"]`)
#102
RalfG
opened
3 weeks ago
1
Recognize .pep.xml files
#101
levitsky
closed
1 week ago
2
pepXML modifications are offset by one
#100
nnalpas
closed
1 week ago
1
Parse idxmls with no spectra file info
#99
jonasscheid
closed
1 month ago
2
Various IO fixes
#98
RalfG
closed
2 months ago
1
Fix column name `Peptide Monoisotopic Mass` in FlashLFQ writing
#97
RalfG
closed
2 months ago
1
Add reader and writer for FlashLFQ
#96
RalfG
closed
2 months ago
1
Peptidoform: Add modified_sequence property
#95
RalfG
closed
2 months ago
1
Percolator fixes: ScanNr writing and inferring style from file extension
#94
RalfG
closed
2 months ago
1
`Peptidoform`: Add property/method to extract modified sequence without charge state
#93
RalfG
closed
2 months ago
1
NoneType object is not subcriptable
#92
prvst
closed
1 month ago
7
Update changelog
#91
RalfG
closed
3 months ago
0
Version bump
#90
RalfG
closed
3 months ago
1
Implement eq and getitem dunder methods for Peptidoform
#89
RalfG
closed
3 months ago
1
Improve TSV reading error handling
#88
RalfG
closed
3 months ago
1
comet support
#87
paretje
closed
4 months ago
1
fix warning when parsing tsv
#85
paretje
closed
4 months ago
0
Add indexing methods to psm_list object
#84
ArthurDeclercq
closed
3 months ago
1
pepXML or mzIdentML from Comet
#86
jke000
closed
4 months ago
3
fix parsing PSMs and complete protein names in XTandem
#83
julianu
closed
4 months ago
2
Remove temporary patch for caching Proforma modification resolvers
#82
RalfG
closed
6 months ago
1
Add Parquet reading and writing for efficient storage of PSM lists
#81
RalfG
closed
6 months ago
1
Update publish workflow to use build or setuptools instead of flit.
#80
RalfG
closed
7 months ago
0
Cache modification resolvers (temporary patch); version bump
#79
RalfG
closed
7 months ago
0
Project and CI changes
#78
RalfG
closed
7 months ago
1
Investigate parsing of mzIdentML `SubstituteModification` entries
#77
RalfG
opened
7 months ago
0
io.proteoscape: Parse filename into PSM run field
#76
RalfG
closed
7 months ago
0
ProteoScape / TIMScore improvements
#75
RalfG
closed
7 months ago
1
idXML updates
#74
RalfG
closed
7 months ago
0
Various bug fixes
#73
ArthurDeclercq
closed
7 months ago
1
Add support for globally-defined terminal modifications
#71
RalfG
closed
8 months ago
0
Add TIMScore Parquet support
#70
RalfG
closed
7 months ago
1
Fixes in `io.xtandem`
#69
RalfG
closed
8 months ago
0
Infer encoding of text-based files?
#68
RalfG
opened
9 months ago
0
Question: Best way to get seperate MSGF+ results (for target and decoy) to one psm_list
#67
JannikSchneider12
closed
8 months ago
1
`io.tsv`: Replace exception with logging
#66
ArthurDeclercq
closed
8 months ago
1
Question: How to deal with percolator output (xml)
#65
JannikSchneider12
closed
9 months ago
0
Getting Name Error with MSGFplus mzid file
#72
thulasis
closed
3 months ago
2
Add support for newer PD MSF file versions
#64
RalfG
opened
11 months ago
0
Fix bug in xtandem reader
#63
RalfG
closed
11 months ago
1
Fix xtandem `run` value parsing; fix renaming negative mass modifications
#62
ArthurDeclercq
closed
1 year ago
1
Convert numpy objects to float in idxml writer
#61
jonasscheid
closed
1 year ago
1
Updating metaValues of PeptideHits with numpy objects crashes in idxml writer
#60
jonasscheid
closed
1 year ago
0
Xtandem run fix
#59
ArthurDeclercq
closed
1 year ago
1
Add score_key argument to XTandemReader
#57
RalfG
closed
1 year ago
1
Fix reading of pepXML files without RT
#56
RalfG
closed
1 year ago
0
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