Ecosyste.ms: Issues

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GitHub / compomics/ms2rescore issues and pull requests

#100 - Suggestions for Ion mobility MS data

Issue - State: closed - Opened by frankligy over 1 year ago - 3 comments
Labels: question

#99 - WIP: Move inferring of spectrum path to parsing psm list?

Pull Request - State: open - Opened by RalfG over 1 year ago

#98 - Config file for maxquant example in v3.0.0-dev4

Issue - State: closed - Opened by veitveit over 1 year ago - 1 comment

#97 - Multiple id input files

Pull Request - State: closed - Opened by ArthurDeclercq over 1 year ago

#96 - Add and update examples (move data to external site, add config files)

Pull Request - State: closed - Opened by RalfG over 1 year ago

#95 - Add `ionmob` feature generator

Pull Request - State: closed - Opened by RalfG over 1 year ago

#94 - MS-GF+ms2rescore pipeline doesn't run

Issue - State: open - Opened by Hassan-1991 over 1 year ago - 1 comment
Labels: v2

#93 - issue with installation

Issue - State: open - Opened by Parniyan-M over 1 year ago - 2 comments
Labels: GUI, v2

#91 - Created msamanda.py and updated __init__.py

Pull Request - State: closed - Opened by louisebuur over 1 year ago

#90 - Couldn't parse MaxQuant modifications in "Modified Sequence" column in CLI

Issue - State: open - Opened by widmersimon over 1 year ago - 1 comment
Labels: v2

#89 - Not able to run ms2resore through command line for this repo examples

Issue - State: closed - Opened by rolivella over 1 year ago - 6 comments
Labels: v2

#87 - Tkinter gui

Pull Request - State: closed - Opened by ArthurDeclercq almost 2 years ago - 1 comment

#86 - Suggest correction for comet pin file

Issue - State: closed - Opened by progistar about 2 years ago - 1 comment

#85 - Issue in selecting the mgf file of the spectrum file in GUI

Issue - State: open - Opened by eunice1029 about 2 years ago - 1 comment
Labels: bug, GUI, v2

#84 - v3

Pull Request - State: closed - Opened by RalfG about 2 years ago

#83 - Allow rescoring of multiple hits per spectrum

Issue - State: closed - Opened by JB91451 over 2 years ago - 2 comments
Labels: feature

#82 - Error parsing scan number from mgf file

Issue - State: closed - Opened by Hassan-1991 over 2 years ago - 1 comment
Labels: question, v2

#81 - PTM information is lost in pin and pout

Issue - State: closed - Opened by caetera over 2 years ago - 2 comments
Labels: bug, refactoring

#80 - Wrong indexing during parsing MGF titles and retention times

Issue - State: closed - Opened by caetera over 2 years ago - 2 comments
Labels: bug, v2

#79 - IDFileParserError: Could not map all MGF retention times to spectrum indices (using MSGF+ pipeline)

Issue - State: closed - Opened by aarmso over 2 years ago - 2 comments
Labels: bug, v2

#78 - Error while running command line ms2rescore

Issue - State: closed - Opened by rolivella over 2 years ago - 1 comment

#77 - Plotting fix

Pull Request - State: closed - Opened by ArthurDeclercq over 2 years ago

#76 - Fix gui maxquant modification parsing error

Pull Request - State: closed - Opened by RalfG over 2 years ago
Labels: bug

#75 - Fix gui maxquant modification parsing error

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

#74 - Filtering of PSMs from MaxQuant Search

Issue - State: closed - Opened by jamc1996 over 2 years ago - 2 comments
Labels: enhancement

#73 - Proteome Discoverer node / PSM file support

Issue - State: closed - Opened by rolivella over 2 years ago - 4 comments
Labels: question, feature

#72 - Rich CLI output; Percolator changes; minor fixes

Pull Request - State: closed - Opened by RalfG over 2 years ago
Labels: enhancement, refactoring

#71 - Plotting percolator weights

Pull Request - State: closed - Opened by ArthurDeclercq over 2 years ago - 3 comments
Labels: enhancement

#70 - Comet pin file fixes

Pull Request - State: closed - Opened by ArthurDeclercq over 2 years ago

#69 - MS²Rescore ignores false run percolator flag

Issue - State: closed - Opened by ArthurDeclercq over 2 years ago - 1 comment
Labels: bug, v2

#68 - Remove temporary setting of NUMEXPR_MAX_THREADS in ms2rescore

Issue - State: closed - Opened by RalfG over 2 years ago - 1 comment
Labels: refactoring

#67 - Fix/comet pin

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

#66 - Peaks pipeline update

Pull Request - State: closed - Opened by ArthurDeclercq over 2 years ago
Labels: bug, enhancement

#65 - Add weights plotting to figure plots

Issue - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: enhancement

#64 - remove redundancy mgf title parser

Issue - State: closed - Opened by ArthurDeclercq almost 3 years ago - 1 comment
Labels: refactoring

#63 - Minor fixes

Pull Request - State: closed - Opened by RalfG almost 3 years ago
Labels: refactoring

#62 - GUI shell fix

Pull Request - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: GUI

#61 - Ignore FutureWarning and DeprecationWarning in GUI logs

Issue - State: closed - Opened by ArthurDeclercq almost 3 years ago

#60 - Refactor modification parsing in PeptideShaker pipeline

Issue - State: closed - Opened by RalfG almost 3 years ago - 1 comment
Labels: enhancement, refactoring

#59 - install without gui?

Issue - State: closed - Opened by Seb-Leb almost 3 years ago - 2 comments

#58 - PeptideShaker pipeline

Pull Request - State: closed - Opened by Seb-Leb almost 3 years ago - 1 comment

#57 - PeaksXPro output compatibility

Pull Request - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: bug, enhancement

#56 - peptideshaker pipeline name fix

Pull Request - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: bug, GUI

#55 - Percolator subprocess does not run in CLI

Issue - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: bug

#54 - PIN pipeline title matching: `ValueError: cannot convert float NaN to integer`

Issue - State: closed - Opened by thaumP almost 3 years ago - 2 comments

#53 - Error with PEAKS mzid file

Issue - State: closed - Opened by nh2tran almost 3 years ago - 13 comments
Labels: bug, v2

#52 - GUI Windows installation error

Issue - State: closed - Opened by nh2tran almost 3 years ago - 2 comments
Labels: GUI

#51 - Limit charge for one-hot encoded features for charge to limited range

Issue - State: closed - Opened by RalfG almost 3 years ago - 1 comment
Labels: enhancement

#47 - Allow long-form modification labels in MaxQuant parser

Pull Request - State: closed - Opened by RalfG almost 3 years ago
Labels: enhancement

#46 - Avoid pandas deprecation warnings and other minor improvements

Pull Request - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: bug, enhancement, refactoring

#44 - Processing PEAKS XPro output using ms2rescore

Issue - State: closed - Opened by DavidGZ1 almost 3 years ago - 2 comments

#43 - Feature/updated gui

Pull Request - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: bug, enhancement, refactoring

#42 - Add regex pattern option for MGF TITLE field

Pull Request - State: closed - Opened by ArthurDeclercq almost 3 years ago
Labels: enhancement, refactoring

#41 - MaxQuant can have long-format modification notations; does not work in current implementation

Issue - State: closed - Opened by NoeGuilloy almost 4 years ago - 5 comments
Labels: enhancement

#40 - Add token to upload action

Pull Request - State: closed - Opened by RalfG about 3 years ago
Labels: CI

#39 - v2.0.0

Pull Request - State: closed - Opened by RalfG about 3 years ago
Labels: CI

#38 - Failed to install ms2rescore

Issue - State: closed - Opened by Peer2011 about 3 years ago - 2 comments

#37 - Add GUI and windows installer batch scripts

Pull Request - State: closed - Opened by RalfG about 3 years ago
Labels: enhancement

#36 - MS²Rescore requires at least cascade_config version v0.2.0

Issue - State: closed - Opened by RalfG about 3 years ago - 1 comment
Labels: bug

#35 - PEAKS support and various fixes/improvements

Pull Request - State: closed - Opened by ArthurDeclercq over 3 years ago
Labels: bug, enhancement, refactoring

#34 - Allow more flexibility in feature sets configuration

Pull Request - State: closed - Opened by ArthurDeclercq over 3 years ago
Labels: enhancement, refactoring

#33 - Implementation of get_search_engine_features for PeptideShaker input

Issue - State: closed - Opened by KunathBJ almost 4 years ago - 3 comments

#32 - Streamlit webserver

Pull Request - State: closed - Opened by RalfG almost 4 years ago - 1 comment
Labels: enhancement

#31 - Streamline handling of invalid amino acids (B, J, O, U, X, Z)

Issue - State: closed - Opened by RalfG almost 4 years ago
Labels: bug

#30 - v2.0.0-beta.5

Pull Request - State: closed - Opened by RalfG almost 4 years ago
Labels: bug

#29 - v2.0.0-beta.4

Pull Request - State: closed - Opened by RalfG almost 4 years ago
Labels: bug

#28 - v2.0.0-beta.3

Pull Request - State: closed - Opened by RalfG almost 4 years ago
Labels: bug, enhancement

#27 - Add flanking amino acids to PIN output

Issue - State: closed - Opened by RalfG almost 4 years ago - 1 comment
Labels: enhancement

#25 - num_cpus used by MS2PIP

Issue - State: closed - Opened by tivdnbos about 4 years ago - 2 comments

#24 - Percolator "Picked protein FDR (-f)" option requires flanking amino acids in PIN peptide column

Issue - State: closed - Opened by tivdnbos about 4 years ago - 5 comments
Labels: enhancement

#23 - v2.0.0-beta.2

Pull Request - State: closed - Opened by RalfG about 4 years ago

#22 - Test and prepare publishing to PyPI

Pull Request - State: closed - Opened by RalfG about 4 years ago

#21 - Support for C-terminal modifications

Issue - State: closed - Opened by RalfG about 4 years ago - 1 comment
Labels: enhancement

#20 - Add support for C-term mods in MSGF+ and PIN input

Pull Request - State: closed - Opened by RalfG about 4 years ago
Labels: enhancement

#19 - Miscellaneous bugfixes

Pull Request - State: closed - Opened by RalfG about 4 years ago
Labels: bug

#18 - Minor improvements, bugfixes and updated docs, following #14 and #17

Pull Request - State: closed - Opened by RalfG about 4 years ago

#17 - Various id_file_parser improvements and fixes

Pull Request - State: closed - Opened by RalfG over 4 years ago
Labels: bug, refactoring

#16 - Add ID file parsers

Pull Request - State: closed - Opened by ArthurDeclercq over 4 years ago
Labels: enhancement

#15 - Update documentation to reflect changes in #14

Issue - State: closed - Opened by RalfG over 4 years ago

#14 - Bugfixes and refactoring (main runner, pipelines, configuration handling...)

Pull Request - State: closed - Opened by RalfG over 4 years ago
Labels: bug, enhancement, refactoring

#13 - [FeatureRequest] add decoy flag to config file

Issue - State: closed - Opened by tivdnbos over 4 years ago

#12 - Snapshot v0.3.0.dev1

Pull Request - State: closed - Opened by RalfG over 4 years ago

#10 - Add generic PIN pipeline

Pull Request - State: closed - Opened by RalfG over 4 years ago

#9 - Add generic PIN pipeline

Issue - State: closed - Opened by RalfG over 4 years ago
Labels: enhancement

#8 - PeptideShaker pipeline: Propagate observed retention time

Issue - State: closed - Opened by RalfG over 4 years ago
Labels: enhancement

#7 - PeptideShaker pipeline: Parse XLS Extended PSM reports

Issue - State: closed - Opened by RalfG over 4 years ago
Labels: enhancement

#6 - DeepLC integration

Pull Request - State: closed - Opened by RalfG over 4 years ago
Labels: enhancement, refactoring

#5 - Update README.md

Pull Request - State: closed - Opened by anasilviacs almost 6 years ago

#4 - Path should be based on peprec file instead of mgf

Issue - State: closed - Opened by tivdnbos over 6 years ago - 1 comment

#3 - N-terminal modifications should be added according old version of MS2PIP

Issue - State: closed - Opened by tivdnbos over 6 years ago - 1 comment

#2 - Updated and cleaned the entire pipeline

Pull Request - State: closed - Opened by anasilviacs over 6 years ago

#1 - Use a config_file

Pull Request - State: closed - Opened by anasilviacs over 6 years ago