Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / levitsky/pyteomics issues and pull requests
#152 - Improve and document modX terminal group support
Pull Request -
State: open - Opened by levitsky 16 days ago
- 2 comments
#151 - Support for Ion Mobility data from Bruker devices?
Issue -
State: open - Opened by LoponteHF about 1 month ago
- 5 comments
#150 - question about how cvParams are read
Issue -
State: closed - Opened by colin-combe 2 months ago
- 2 comments
#149 - question about ms2 reader
Issue -
State: closed - Opened by colin-combe 2 months ago
- 13 comments
#148 - Add modification caching; Constant terminal mods for ProForma
Pull Request -
State: closed - Opened by mobiusklein 2 months ago
#147 - [proforma] Use cache on modification resolvers
Pull Request -
State: closed - Opened by RalfG 3 months ago
- 8 comments
#146 - xpath in mzIdentML reader behaves differently from other xpath implementations?
Issue -
State: closed - Opened by colin-combe 3 months ago
- 3 comments
#145 - question about memory use with mzIdentML reader
Issue -
State: open - Opened by colin-combe 3 months ago
- 16 comments
#144 - Adjust pickling
Pull Request -
State: closed - Opened by mobiusklein 3 months ago
#143 - [proforma] Modifications cannot be pickled after being resolved
Issue -
State: closed - Opened by RalfG 3 months ago
- 2 comments
#142 - Rename _build_index to build_byte_index
Pull Request -
State: closed - Opened by levitsky 5 months ago
#141 - Fix for #136 is unreleased
Issue -
State: closed - Opened by sjust-seerbio 5 months ago
- 2 comments
#140 - IndexSavingMixin._build_index() is never called by text parsers?
Issue -
State: closed - Opened by levitsky 5 months ago
- 4 comments
#139 - Failing to parse UniProt description with space in gene symbol
Issue -
State: closed - Opened by caetera 5 months ago
- 2 comments
#138 - Add a warning when an empty index is created, customize it for mgf
Pull Request -
State: closed - Opened by levitsky 6 months ago
- 1 comment
#137 - Calculate m/z for proforma in calculate_mass
Pull Request -
State: closed - Opened by levitsky 6 months ago
- 4 comments
#136 - New problem with parsing FASTA files
Issue -
State: closed - Opened by tristanbrown 7 months ago
- 3 comments
#135 - Incorrect expasy rule
Issue -
State: closed - Opened by Karl-Krauth 7 months ago
- 1 comment
#134 - MGF File Loading Error - IndexedMGF Object Empty
Issue -
State: closed - Opened by CCranney 7 months ago
- 3 comments
#133 - Fix UniMod by ID
Pull Request -
State: closed - Opened by mobiusklein 7 months ago
- 2 comments
#132 - [proforma] Unimod modificatons cannot be resolved by ID through psims
Issue -
State: closed - Opened by RalfG 7 months ago
#130 - Mass modification hashing
Pull Request -
State: closed - Opened by mobiusklein 8 months ago
- 1 comment
#129 - If psims is available, use its Unimod because it caches and vendors
Pull Request -
State: closed - Opened by mobiusklein 9 months ago
- 3 comments
#128 - Import of Unimod schema crashes when Unimod is down
Issue -
State: closed - Opened by jonasscheid 9 months ago
- 5 comments
#127 - Deisotoping Methodology - future pyteomics implementation?
Issue -
State: closed - Opened by CCranney 9 months ago
- 2 comments
#126 - Update imports for sqlalchemy v2.0 changes
Pull Request -
State: closed - Opened by RalfG 10 months ago
- 4 comments
#125 - Fix levitsky/pyteomics#124
Pull Request -
State: closed - Opened by sjust-seerbio 10 months ago
#124 - AttributeError: module 'pyteomics.auxiliary' has no attribute 'PytemicsError'
Issue -
State: closed - Opened by sjust-seerbio 10 months ago
- 3 comments
#123 - C-terminal modifications in calculate_mass
Issue -
State: closed - Opened by JB91451 10 months ago
- 2 comments
#122 - MGF Writing error - `TypeError: 'numpy.int64' object is not iterable`
Issue -
State: closed - Opened by CCranney 10 months ago
- 3 comments
#121 - Use metaclass to add __init__ to flavored fasta parsers
Pull Request -
State: closed - Opened by levitsky 10 months ago
#120 - Add raw fasta file header to parsers
Pull Request -
State: closed - Opened by caetera 10 months ago
- 7 comments
#119 - Pandas is now a hard requirement
Issue -
State: closed - Opened by mobiusklein 10 months ago
- 3 comments
#118 - Pandas Version Checking Fails
Issue -
State: closed - Opened by jmmitc06 10 months ago
- 3 comments
#117 - Add optional quantile regression for get_RCs
Pull Request -
State: closed - Opened by markmipt 11 months ago
#116 - Load mzML file with ion mobility
Issue -
State: closed - Opened by mobiotwin 11 months ago
- 4 comments
#115 - The issue of secondary spectrum
Issue -
State: closed - Opened by morestart about 1 year ago
- 12 comments
#113 - Polarity missing from mzMLb parser
Issue -
State: closed - Opened by sorenwacker about 1 year ago
- 2 comments
#112 - Error with version 4.6 when trying to open mzML or mzXML files.
Issue -
State: closed - Opened by sorenwacker about 1 year ago
- 1 comment
#111 - file_mode keyword only param to write mgf function breaks linters
Issue -
State: closed - Opened by hechth about 1 year ago
- 2 comments
#110 - Unable to use map() method in PepXML class
Issue -
State: closed - Opened by freejstone about 1 year ago
- 2 comments
#108 - unable to extract "charge array" with pyteomics.ms2.IndexedMS2
Issue -
State: closed - Opened by irleader over 1 year ago
- 7 comments
#107 - C-terminal modification parsing in ProForma
Issue -
State: closed - Opened by caetera over 1 year ago
- 2 comments
#106 - Fix iteration in example for calculating theoretical fragment m/z
Pull Request -
State: closed - Opened by michabirklbauer over 1 year ago
- 1 comment
#105 - Pass through the decode_binary parameter in read for mzml and mzxml
Pull Request -
State: closed - Opened by mobiusklein over 1 year ago
- 1 comment
#104 - [mzml] `decode_binary` argument documented but not implemented
Issue -
State: closed - Opened by RalfG over 1 year ago
- 1 comment
#102 - Hard-code UniRef keys, remove extra fields created by str.split()
Pull Request -
State: closed - Opened by levitsky over 1 year ago
#101 - Address broader ProForma colon ambiguity
Pull Request -
State: closed - Opened by mobiusklein over 1 year ago
#100 - Incorrect resolving of modification names with semicolon by UnimodModification
Issue -
State: closed - Opened by caetera over 1 year ago
- 2 comments
#99 - Fix issue #98 for colon-containing mods
Pull Request -
State: closed - Opened by mobiusklein over 1 year ago
- 1 comment
#98 - ProForma parser can't handle a modification name with colon if it occurs without ontology prefix
Issue -
State: closed - Opened by levitsky over 1 year ago
- 1 comment
#97 - Extract date stamp of data acquisition?
Issue -
State: closed - Opened by sorenwacker over 1 year ago
- 2 comments
#96 - Module 'pyteomics.proforma' has no attribute 'Proforma'
Issue -
State: closed - Opened by alessandro-vai over 1 year ago
- 1 comment
#95 - Resolve `referenceableParamGroupRef`
Pull Request -
State: closed - Opened by mobiusklein over 1 year ago
- 4 comments
#93 - Hard-code key=value pairs in Uniprot headers as described in the spec
Pull Request -
State: closed - Opened by levitsky over 1 year ago
- 4 comments
#92 - Support slicing ProForma
Pull Request -
State: closed - Opened by mobiusklein over 1 year ago
#91 - [BUG (??)] Terminal modifications are kept regardless of slicing
Issue -
State: closed - Opened by jspaezp over 1 year ago
- 2 comments
#90 - Cannot reproduce Example 4: Spectrum Annotation
Issue -
State: closed - Opened by alessandro-vai over 1 year ago
- 6 comments
#89 - Link to https instead of http
Pull Request -
State: closed - Opened by fabianegli over 1 year ago
#88 - Add installatoin instructions for pyteomics for conda from the bioconda channel
Issue -
State: closed - Opened by fabianegli over 1 year ago
- 7 comments
Labels: documentation
#87 - FDR calculate
Issue -
State: closed - Opened by KKKKK-tech over 1 year ago
- 2 comments
#85 - Improve documentation of Unimod loading and highlight in ProForma
Pull Request -
State: closed - Opened by mobiusklein over 1 year ago
- 5 comments
#84 - use packaging instead of distutils if available
Pull Request -
State: closed - Opened by fabianegli over 1 year ago
#83 - Python 3.10 emmits a DeprecationWarning for distutils LooseVersion
Issue -
State: closed - Opened by fabianegli over 1 year ago
#82 - [Pitch] Include unimod with the release of pyteomics
Issue -
State: closed - Opened by jspaezp over 1 year ago
- 8 comments
#81 - Example 4: Spectrum Annotation appears to be broken
Issue -
State: closed - Opened by wsnoble over 1 year ago
- 3 comments
#79 - [Question] How to get instrument information from mzML
Issue -
State: closed - Opened by jspaezp over 1 year ago
- 2 comments
#78 - Correct the parsing of C-terminal modifications when the last amino acid is also modified
Pull Request -
State: closed - Opened by mobiusklein almost 2 years ago
#77 - [proforma] Final and C-terminal modifications are parsed as one
Issue -
State: closed - Opened by RalfG almost 2 years ago
#76 - fasta .get_by_id method only matching single entry
Issue -
State: closed - Opened by radusuciu about 2 years ago
- 4 comments
#75 - Update to regex for Uniprot Fasta heade rparser
Issue -
State: closed - Opened by hguturu about 2 years ago
- 7 comments
#74 - tandem.DataFrame fails when tandem was run on .cmn input
Issue -
State: closed - Opened by kesinger about 2 years ago
- 2 comments
#73 - Is there an idXML writer anywhere? what about a schema?
Issue -
State: closed - Opened by trishorts about 2 years ago
- 2 comments
#72 - How to convert the modified scans into an mzXML file?
Issue -
State: closed - Opened by Mnago over 2 years ago
- 1 comment
#71 - typo?
Pull Request -
State: closed - Opened by superrino130 over 2 years ago
- 1 comment
#70 - Switch USI test backend
Pull Request -
State: closed - Opened by mobiusklein over 2 years ago
- 1 comment
#69 - Fix generic modification resolver
Pull Request -
State: closed - Opened by mobiusklein over 2 years ago
- 1 comment
#68 - [proforma] Unresolvable modification results in non-descriptive error when accessing `.mass` property
Issue -
State: closed - Opened by RalfG over 2 years ago
- 1 comment
#67 - Explicitly close the thread pool in PROXIAggregator on GC
Pull Request -
State: closed - Opened by mobiusklein over 2 years ago
- 1 comment
#66 - ThreadPool in PROXIAggregator not closed
Issue -
State: closed - Opened by bittremieux over 2 years ago
- 2 comments
#65 - can't get m/z array and intensity array
Issue -
State: closed - Opened by morestart over 2 years ago
- 5 comments
#64 - Restores IndexedIterfind.map functionality
Pull Request -
State: closed - Opened by mobiusklein over 2 years ago
#63 - Proforma modification hashing and other fixes
Pull Request -
State: closed - Opened by mobiusklein over 2 years ago
- 2 comments
#62 - [proforma] Make modification object hashable
Issue -
State: closed - Opened by RalfG over 2 years ago
- 6 comments
#61 - Implement `charge_carrier` and `absolute` arguments for m/z calculation
Pull Request -
State: closed - Opened by levitsky over 2 years ago
- 8 comments
#60 - mass calculation with negative charge
Issue -
State: closed - Opened by mgleeming over 2 years ago
- 3 comments
Labels: enhancement, good first issue
#58 - DOCFIX Remove trailing "s" from example code
Pull Request -
State: closed - Opened by mobiusklein almost 3 years ago
#57 - Document the unit handling and controlled vocabulary string features
Pull Request -
State: closed - Opened by mobiusklein almost 3 years ago
#56 - mzML reader for RT ambiguous units
Issue -
State: closed - Opened by mwang87 almost 3 years ago
- 4 comments
#55 - Handle cases where the PROXI server responds with properly typed numerical values for attributes
Pull Request -
State: closed - Opened by mobiusklein almost 3 years ago
#54 - Shuffling that preserves some amino acids
Pull Request -
State: closed - Opened by caetera almost 3 years ago
- 2 comments
#53 - Update default featureXML schema_info and version, add overrides
Pull Request -
State: closed - Opened by levitsky almost 3 years ago
#52 - Warning is triggered even with `use_index=False`
Issue -
State: closed - Opened by hguturu almost 3 years ago
- 4 comments
#51 - Fix ProForma Parsing and Update Docs
Pull Request -
State: closed - Opened by mobiusklein almost 3 years ago
- 1 comment
#50 - `spectrum_reference` should not be a int in `featureXML`
Issue -
State: closed - Opened by hguturu almost 3 years ago
- 8 comments
#48 - Properly detect non-standard array name when it is a term value
Pull Request -
State: closed - Opened by mobiusklein about 3 years ago
#47 - Problems with loading Unimod into PostgreSQL
Issue -
State: open - Opened by radusuciu about 3 years ago
- 2 comments
#45 - PROXIAggregator may also return tagged responses instead of merging
Pull Request -
State: closed - Opened by mobiusklein about 3 years ago
#44 - mzident parser
Issue -
State: closed - Opened by jschmacht about 3 years ago
- 3 comments