Ecosyste.ms: Issues

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GitHub / compomics/ms2rescore issues and pull requests

#206 - Update to v4 of the artifact actions

Issue - State: open - Opened by RalfG about 2 months ago
Labels: CI

#205 - Fix im2deep import

Pull Request - State: closed - Opened by ArthurDeclercq 2 months ago
Labels: bug

#204 - im2deep dependency broken

Issue - State: closed - Opened by MatthewThe 2 months ago - 1 comment
Labels: bug

#202 - Add MS²Rescore version in written full config file

Issue - State: open - Opened by RalfG 3 months ago
Labels: enhancement

#201 - GUI: Allow spaces in input files

Issue - State: open - Opened by RalfG 3 months ago

#200 - Add functionality to save mokapot models

Pull Request - State: closed - Opened by SamvPy 4 months ago

#199 - Pin pyOpenMS

Pull Request - State: closed - Opened by RalfG 4 months ago
Labels: bug, dependencies

#198 - Pin DeepLC version to <3.1, avoiding calibration bug

Pull Request - State: closed - Opened by RalfG 4 months ago
Labels: bug, dependencies

#197 - Pin DeepLC version to <3.1, avoiding calibration bug

Pull Request - State: closed - Opened by RalfG 4 months ago
Labels: bug, dependencies

#195 - Update im2deep utf8 error

Pull Request - State: closed - Opened by ArthurDeclercq 4 months ago
Labels: bug

#192 - Handle None in psm_list['rescoring_features']

Issue - State: open - Opened by rodvrees 4 months ago

#191 - Fix incorrect decoy pattern configuration in docs

Pull Request - State: closed - Opened by rodvrees 5 months ago - 1 comment
Labels: documentation

#190 - Logging bug in GUI in debug mode

Issue - State: open - Opened by RalfG 5 months ago - 2 comments
Labels: bug

#189 - Update dependencies

Pull Request - State: closed - Opened by RalfG 5 months ago
Labels: dependencies

#188 - Fix encoding error in DeepLC logging

Pull Request - State: closed - Opened by RalfG 5 months ago
Labels: bug

#187 - Docs: Fix README URLs to documentation pages

Pull Request - State: closed - Opened by RalfG 5 months ago
Labels: documentation

#186 - Switch to FlashLFQ output from psm_utils

Pull Request - State: closed - Opened by RalfG 5 months ago
Labels: enhancement

#185 - UnicodeEncodeError: 'ascii' codec can't encode characters in position ...

Issue - State: closed - Opened by prvst 5 months ago - 1 comment
Labels: bug

#184 - support gzipped spectra files

Pull Request - State: closed - Opened by paretje 5 months ago - 1 comment
Labels: feature

#183 - 'charmap' codec can't encode characters in position XX

Issue - State: closed - Opened by JesusCastano01 5 months ago - 3 comments
Labels: bug

#182 - Catch IndexError in Qvality when PEP cannot be calculated

Pull Request - State: closed - Opened by RalfG 5 months ago
Labels: bug

#181 - Minor doc updates

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: documentation

#180 - Fix ruff checks for tutorial notebook

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: CI

#178 - Spectrum feature generator

Pull Request - State: open - Opened by ArthurDeclercq 6 months ago - 2 comments
Labels: feature

#177 - pull main in spectrum-feature-generator

Pull Request - State: closed - Opened by ArthurDeclercq 6 months ago

#176 - Fix bug in TIMS²Rescore configuration priority

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: bug

#175 - Improve GUI user experience

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: GUI

#173 - Fix Windows installer test (missing ionmob dep)

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: CI

#172 - Fix: Pass IM2Deep config in GUI

Pull Request - State: closed - Opened by ArthurDeclercq 6 months ago
Labels: bug, GUI

#171 - im2deep not working with the GUI

Issue - State: closed - Opened by AlexandreBurel 6 months ago - 1 comment
Labels: bug, GUI

#170 - SSL certificate error

Issue - State: closed - Opened by prvst 6 months ago - 4 comments

#169 - Limit Percolator processes to 128 (fixes #117)

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: enhancement

#167 - build and publish docker image

Pull Request - State: closed - Opened by paretje 6 months ago
Labels: CI

#165 - Various issues while processing PeptideShaker mzIdentML results

Issue - State: closed - Opened by ofleitas 6 months ago - 8 comments
Labels: question

#163 - Fix ionmob in Windows installer

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: CI, GUI

#162 - Refactor parsing of precursor data from spectrum files

Pull Request - State: closed - Opened by RalfG 6 months ago
Labels: enhancement, refactoring

#161 - TIMS²Rescore-related fixes and improvements

Pull Request - State: closed - Opened by RalfG 7 months ago

#160 - Update tims2rescore documentation

Pull Request - State: closed - Opened by RalfG 7 months ago

#159 - Add docs for isobaric formula modifications

Pull Request - State: closed - Opened by RalfG 7 months ago - 1 comment

#158 - Implement better logging for PSM ID to spectrum ID matching

Issue - State: open - Opened by RalfG 7 months ago - 1 comment
Labels: enhancement

#155 - Validate that all modifications are resolvable

Issue - State: open - Opened by RalfG 7 months ago
Labels: enhancement

#154 - Reports of error in `freeze_support` with Windows installer

Issue - State: open - Opened by RalfG 7 months ago
Labels: bug, GUI

#153 - Target-decoy competition settings

Issue - State: closed - Opened by MatteoLacki 8 months ago - 1 comment
Labels: question

#152 - pepXML or mzIdentML from Comet

Issue - State: open - Opened by jke000 8 months ago

#150 - MS2PIPFeatureGenerator and DeepLCFeatureGenerator, provide a progress callback

Issue - State: open - Opened by vrkosk 8 months ago - 1 comment
Labels: enhancement

#149 - pyopenms DLL issue

Issue - State: closed - Opened by AUldry 8 months ago - 1 comment
Labels: bug, GUI, upstream

#148 - Parameters for rescoring peptidomics data

Issue - State: closed - Opened by Dmorgen 9 months ago - 5 comments

#147 - error running rescore - tries to download something?

Issue - State: closed - Opened by Dmorgen 9 months ago - 2 comments

#145 - Scipy dependency issue in Windows Installer for v3.0.3

Issue - State: closed - Opened by RalfG 10 months ago - 2 comments

#144 - Fixes for MS²Rescore report

Pull Request - State: closed - Opened by ArthurDeclercq 10 months ago

#143 - Docs: Add instructions for fixed terminal modifications

Pull Request - State: closed - Opened by RalfG 10 months ago
Labels: documentation

#142 - TIMS²Rescore

Pull Request - State: closed - Opened by RalfG 10 months ago
Labels: enhancement

#141 - Use Rust for parsing spectrum files

Pull Request - State: closed - Opened by RalfG 10 months ago
Labels: bug, enhancement

#140 - Could not find matching spectra

Issue - State: closed - Opened by JesusCastano01 10 months ago - 2 comments
Labels: question

#139 - Model slowly downloaded

Issue - State: closed - Opened by danyunghsu 10 months ago - 2 comments
Labels: question

#138 - Various minor improvements

Pull Request - State: closed - Opened by RalfG 10 months ago
Labels: enhancement

#137 - Various minor improvements

Pull Request - State: closed - Opened by RalfG 10 months ago

#136 - MSMS Parsing with MaxQuant

Issue - State: closed - Opened by JesusCastano01 10 months ago - 3 comments
Labels: question, upstream

#135 - Add user control for whether models are downloaded automatically

Issue - State: open - Opened by vrkosk 11 months ago - 2 comments
Labels: enhancement

#134 - Specify custom model directory in MS2PIPFeatureGenerator

Issue - State: closed - Opened by vrkosk 11 months ago
Labels: enhancement

#133 - downgrade pyteomics version in pyproject.toml

Pull Request - State: closed - Opened by ArthurDeclercq 11 months ago - 1 comment

#132 - Pull main in timsRescore

Pull Request - State: closed - Opened by ArthurDeclercq 11 months ago

#131 - Support ppm as MS2 tolerance in MS2PIPFeatureGenerator

Issue - State: open - Opened by vrkosk 11 months ago

#130 - Uncaught exception in DeepLCFeatureGenerator if not enough peptides for calibration set

Issue - State: closed - Opened by vrkosk 11 months ago - 3 comments
Labels: bug, enhancement

#129 - Persistent warning about OPENMS_DATA_PATH

Issue - State: closed - Opened by vrkosk 11 months ago - 4 comments
Labels: upstream

#128 - Fatal pickling exception when using [UNIMOD:nn] identifier in ProForma string

Issue - State: closed - Opened by vrkosk 11 months ago - 7 comments
Labels: bug, upstream

#127 - Update README.md

Pull Request - State: closed - Opened by RalfG 11 months ago
Labels: documentation

#126 - Cannot resolve mass for invalid amino acid

Issue - State: closed - Opened by ArthurDeclercq 11 months ago - 1 comment
Labels: bug

#125 - Adding peptide n-terminal fixed modification

Issue - State: closed - Opened by XiuyuanChen1 11 months ago - 1 comment
Labels: enhancement

#124 - Add feature descriptions to documentation

Issue - State: closed - Opened by Guitou1 11 months ago - 1 comment
Labels: documentation

#123 - Fix GUI on Linux systems

Pull Request - State: closed - Opened by RalfG 11 months ago

#122 - Extend support for timsTOF instruments

Pull Request - State: closed - Opened by RalfG 12 months ago
Labels: bug, enhancement, feature

#121 - merge im2deep into timsrescore branch

Pull Request - State: closed - Opened by ArthurDeclercq 12 months ago

#120 - Update IM key when parsing spectra

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 1 comment

#119 - Better handle exceptions when generating report

Pull Request - State: closed - Opened by RalfG about 1 year ago
Labels: enhancement

#118 - GUI crashes on linux system

Issue - State: closed - Opened by ArthurDeclercq about 1 year ago - 1 comment

#117 - When using Percolator with more than 128 threads, MS2Rescore returns empty pout files

Issue - State: closed - Opened by tivdnbos about 1 year ago
Labels: enhancement

#116 - ms2rescore graphical user interface

Issue - State: closed - Opened by DaliJarboui about 1 year ago - 1 comment
Labels: CI

#115 - Getting Name Error with MSGFplus mzid file

Issue - State: open - Opened by thulasis about 1 year ago

#114 - Issue with QC report for percolator

Issue - State: closed - Opened by juslm about 1 year ago
Labels: bug

#113 - Update DeepLC integration to send PSMList object instead of peprec dataframe

Issue - State: closed - Opened by RalfG about 1 year ago
Labels: enhancement

#112 - Support different levels of confidence estimates when using mokapot

Issue - State: open - Opened by jonasscheid about 1 year ago - 2 comments
Labels: feature

#111 - Lack of documentation on the command line interface

Issue - State: closed - Opened by Guitou1 about 1 year ago - 2 comments
Labels: question

#110 - Finalize documentation for 3.0

Pull Request - State: closed - Opened by RalfG about 1 year ago
Labels: documentation

#107 - Cannot resolve mass for modification

Issue - State: closed - Opened by MatteoLacki about 1 year ago - 11 comments
Labels: bug

#106 - Correctly handle peptides with invalid residues (BJOUXZ)

Issue - State: closed - Opened by RalfG about 1 year ago - 2 comments
Labels: enhancement

#105 - Add lower-rank filtering option

Issue - State: closed - Opened by RalfG about 1 year ago - 1 comment
Labels: feature

#104 - Improve logging of modification mapping functionality

Issue - State: closed - Opened by RalfG over 1 year ago - 1 comment
Labels: enhancement

#102 - Fix build of Windows PyInstaller

Pull Request - State: closed - Opened by RalfG over 1 year ago
Labels: bug, CI