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levitsky
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pyteomics
Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
http://pyteomics.readthedocs.io
Apache License 2.0
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ProForma parser can't handle a modification name with colon if it occurs without ontology prefix
#98
levitsky
closed
1 year ago
1
Extract date stamp of data acquisition?
#97
sorenwacker
closed
1 year ago
2
Module 'pyteomics.proforma' has no attribute 'Proforma'
#96
alessandro-vai
closed
1 year ago
1
Resolve `referenceableParamGroupRef`
#95
mobiusklein
closed
1 year ago
4
RE
#94
mafreitas
closed
1 year ago
6
Hard-code key=value pairs in Uniprot headers as described in the spec
#93
levitsky
closed
1 year ago
4
Support slicing ProForma
#92
mobiusklein
closed
1 year ago
0
[BUG (??)] Terminal modifications are kept regardless of slicing
#91
jspaezp
closed
1 year ago
2
Cannot reproduce Example 4: Spectrum Annotation
#90
alessandro-vai
closed
1 year ago
6
Link to https instead of http
#89
fabianegli
closed
1 year ago
0
Add installatoin instructions for pyteomics for conda from the bioconda channel
#88
fabianegli
closed
1 year ago
7
FDR calculate
#87
KKKKK-tech
closed
1 year ago
2
Improve documentation of Unimod loading and highlight in ProForma
#85
mobiusklein
closed
1 year ago
5
use packaging instead of distutils if available
#84
fabianegli
closed
1 year ago
0
Python 3.10 emmits a DeprecationWarning for distutils LooseVersion
#83
fabianegli
closed
1 year ago
0
[Pitch] Include unimod with the release of pyteomics
#82
jspaezp
closed
1 year ago
8
Example 4: Spectrum Annotation appears to be broken
#81
wsnoble
closed
1 year ago
3
[Question] How to get instrument information from mzML
#79
jspaezp
closed
1 year ago
2
Correct the parsing of C-terminal modifications when the last amino acid is also modified
#78
mobiusklein
closed
1 year ago
0
[proforma] Final and C-terminal modifications are parsed as one
#77
RalfG
closed
1 year ago
0
fasta .get_by_id method only matching single entry
#76
radusuciu
closed
2 years ago
4
Update to regex for Uniprot Fasta heade rparser
#75
hguturu
closed
1 year ago
7
tandem.DataFrame fails when tandem was run on .cmn input
#74
kesinger
closed
2 years ago
2
Is there an idXML writer anywhere? what about a schema?
#73
trishorts
closed
2 years ago
2
How to convert the modified scans into an mzXML file?
#72
Mnago
closed
1 year ago
1
typo?
#71
superrino130
closed
2 years ago
1
Switch USI test backend
#70
mobiusklein
closed
2 years ago
1
Fix generic modification resolver
#69
mobiusklein
closed
2 years ago
1
[proforma] Unresolvable modification results in non-descriptive error when accessing `.mass` property
#68
RalfG
closed
2 years ago
1
Explicitly close the thread pool in PROXIAggregator on GC
#67
mobiusklein
closed
2 years ago
1
ThreadPool in PROXIAggregator not closed
#66
bittremieux
closed
2 years ago
2
can't get m/z array and intensity array
#65
morestart
closed
2 years ago
5
Restores IndexedIterfind.map functionality
#64
mobiusklein
closed
2 years ago
0
Proforma modification hashing and other fixes
#63
mobiusklein
closed
2 years ago
2
[proforma] Make modification object hashable
#62
RalfG
closed
2 years ago
6
Implement `charge_carrier` and `absolute` arguments for m/z calculation
#61
levitsky
closed
2 years ago
8
mass calculation with negative charge
#60
mgleeming
closed
2 years ago
3
DOCFIX Remove trailing "s" from example code
#58
mobiusklein
closed
2 years ago
0
Document the unit handling and controlled vocabulary string features
#57
mobiusklein
closed
2 years ago
0
mzML reader for RT ambiguous units
#56
mwang87
closed
2 years ago
4
Handle cases where the PROXI server responds with properly typed numerical values for attributes
#55
mobiusklein
closed
2 years ago
0
Shuffling that preserves some amino acids
#54
caetera
closed
2 years ago
2
Update default featureXML schema_info and version, add overrides
#53
levitsky
closed
2 years ago
0
Warning is triggered even with `use_index=False`
#52
hguturu
closed
2 years ago
4
Fix ProForma Parsing and Update Docs
#51
mobiusklein
closed
2 years ago
1
`spectrum_reference` should not be a int in `featureXML`
#50
hguturu
closed
2 years ago
8
Properly detect non-standard array name when it is a term value
#48
mobiusklein
closed
3 years ago
0
Problems with loading Unimod into PostgreSQL
#47
radusuciu
opened
3 years ago
2
PROXIAggregator may also return tagged responses instead of merging
#45
mobiusklein
closed
3 years ago
0
mzident parser
#44
jschmacht
closed
3 years ago
3
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