grosenberger/easypqp issues and pull requests

#108 - Could you please release version 0.1.41

Issue - State: closed - Opened by fcyu 11 months ago - 3 comments

#107 - Fix another bug due to 0 IDs in the pepxml file.

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

#106 - Update main.py

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

#105 - Multiple bugfixes and improvements

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

#104 - Issue with EasyPQP 0.1.39

Issue - State: closed - Opened by JesusCastano01 over 1 year ago - 1 comment

#103 - Assertion Error

Issue - State: closed - Opened by ngirardi over 1 year ago - 2 comments

#102 - KeyError: 'run_id'

Issue - State: closed - Opened by jsalbin1 over 1 year ago - 4 comments

#101 - [FIX] Resolve product m/z conflicts

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

#100 - Speed and memory optimization for the FragPipe DIA workflow.

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

#99 - Feature/openswathdecoygenerator

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

#98 - Feature/openswathassaygenerator

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

#97 - Feature/tests

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

#96 - Update the unimod.xml to the latest version.

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

#95 - Transitions with the same PrecursorMz and different annotations

Issue - State: closed - Opened by jcharkow over 1 year ago - 5 comments

#94 - Feature/targetedfileconverter

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

#93 - Modify the neutral loss ions to make it compatible with DIA-NN

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

#92 - Fix a scan number extraction bug for the non-Thermo vendors.

Pull Request - State: closed - Opened by fcyu about 2 years ago - 1 comment

#91 - [FIX] Fix UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 Er…

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

#90 - Making some changes to be compatible with the latest FragPipe.

Pull Request - State: closed - Opened by fcyu about 2 years ago - 1 comment

#89 - easypqp filter-unimod UnicodeDecodeError

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

#88 - Feature/filter unimod

Pull Request - State: closed - Opened by singjc over 2 years ago - 1 comment

#87 - [FEATURE] Add module to filter a unimod XML database file

Pull Request - State: closed - Opened by singjc over 2 years ago - 1 comment

#86 - Why to exclude massdiff when convering pepXML

Issue - State: closed - Opened by shubham1637 over 2 years ago - 1 comment

#85 - Not able to install in Python3.10

Issue - State: closed - Opened by chinmayaNK22 over 2 years ago - 6 comments

#84 - [FEATURE] optional calibration

Pull Request - State: closed - Opened by jcharkow over 2 years ago - 1 comment

#83 - Documentation for integration with TPP

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

#82 - Fix unify mod masses

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

#81 - Negative retention time numbers?

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

#80 - Unify mod masses

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

#79 - fix unannotated mods

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

#78 - Limit to number of files as input to easyPQP

Issue - State: closed - Opened by jonathan-krieger-bruker over 2 years ago

#77 - output alignment

Pull Request - State: closed - Opened by guoci almost 3 years ago

#76 - Controlling the number of threads for parsing

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

#75 - workaround `loky` issue

Pull Request - State: closed - Opened by guoci almost 3 years ago - 2 comments

#74 - Building library from independent FragPipe output

Issue - State: closed - Opened by plbaldoni about 3 years ago - 4 comments

#73 - optimize annotation code for mgf files

Pull Request - State: closed - Opened by guoci over 3 years ago

#72 - silence warnings from `sm.nonparametric.lowess`

Pull Request - State: closed - Opened by guoci over 3 years ago

#71 - Not sure which files to use.

Issue - State: closed - Opened by PatrickvanZalm over 3 years ago - 2 comments

#70 - optimize annotation code

Pull Request - State: closed - Opened by guoci over 3 years ago

#69 - minor refactoring

Pull Request - State: closed - Opened by guoci over 3 years ago

#68 - optimize `convert` command

Pull Request - State: closed - Opened by guoci over 3 years ago

#67 - filter_psms

Pull Request - State: closed - Opened by guoci over 3 years ago - 2 comments

#66 - fix skipped runs

Pull Request - State: closed - Opened by guoci over 3 years ago

#65 - fix string comparison

Pull Request - State: closed - Opened by guoci over 3 years ago

#64 - include unimod.xml in sdist

Pull Request - State: closed - Opened by guoci over 3 years ago

#63 - round mass shifts.

Pull Request - State: closed - Opened by guoci over 3 years ago

#62 - add monomeric masses for O(pyrrolysine) and U(selenocysteine)

Pull Request - State: closed - Opened by guoci over 3 years ago

#61 - [FIX] argument parsing

Pull Request - State: closed - Opened by guoci over 3 years ago

#60 - [FIX] fragment_* arguments

Pull Request - State: closed - Opened by guoci over 3 years ago

#59 - write reference run IM tsv file

Pull Request - State: closed - Opened by guoci over 3 years ago

#58 - [FIX] fc3c4a59c2bf36dfb295851de109bb12b0c88293

Pull Request - State: closed - Opened by guoci over 3 years ago

#57 - allow missing peptide probablity

Pull Request - State: closed - Opened by guoci over 3 years ago

#56 - fix long command line issue

Pull Request - State: closed - Opened by guoci over 3 years ago - 1 comment

#55 - Error Handling Modifications not in UniMod

Issue - State: closed - Opened by xLinkKnight over 3 years ago - 7 comments

#54 - write reference run RT tsv file

Pull Request - State: closed - Opened by guoci over 3 years ago - 1 comment

#53 - TPP C-term mass correction

Pull Request - State: closed - Opened by grosenberger over 3 years ago

#52 - Set minimum version for `pyOpenMS`

Pull Request - State: closed - Opened by guoci over 3 years ago

#51 - easyPQP(0.1.9) cannot be installed in Fragpipe(version 15)

Issue - State: closed - Opened by lyumengge over 3 years ago - 1 comment

#50 - There are errors in running EasyPQP

Issue - State: closed - Opened by xuezhangzhi over 3 years ago - 6 comments

#49 - Set a minimum version for `pandas`

Pull Request - State: closed - Opened by guoci over 3 years ago

#48 - [FIX] Use delta mass instead of massdiff with enable_unannotated

Pull Request - State: closed - Opened by grosenberger over 3 years ago

#47 - [fix] parse rank from basename instead of path

Pull Request - State: closed - Opened by guoci almost 4 years ago

#46 - Bug in im reference file error checking

Pull Request - State: closed - Opened by jcharkow almost 4 years ago - 1 comment

#45 - determine mgf header format at parse

Pull Request - State: closed - Opened by guoci almost 4 years ago

#44 - Is there any way to filter ions in the library conforming to the down criterions like spectrast2tsv?

Issue - State: closed - Opened by lifeinfo almost 4 years ago - 1 comment

#43 - [FIX] cross OS issue for os.path.basename

Pull Request - State: closed - Opened by guoci almost 4 years ago

#42 - retention time reversed

Issue - State: closed - Opened by zhutiansheng almost 4 years ago - 6 comments

#41 - [FIX] NameError: name 'enable_unannotated' is not defined

Pull Request - State: closed - Opened by guoci almost 4 years ago

#40 - iRT alignment issue

Issue - State: closed - Opened by aparnasrini03 almost 4 years ago - 2 comments

#39 - number of CPUS

Issue - State: closed - Opened by cguetot almost 4 years ago - 1 comment

#38 - got an error by enabling specific losses

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

#37 - can easypqp build library with irt

Issue - State: closed - Opened by lifeinfo about 4 years ago - 16 comments

#36 - rm comet specific scores

Pull Request - State: closed - Opened by Leon-Bichmann about 4 years ago - 1 comment

#35 - MSFragger SL Generation

Issue - State: closed - Opened by xLinkKnight about 4 years ago - 1 comment

#34 - increase lowess fraction if it is too small

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

#33 - how can easypqp control fdr

Issue - State: closed - Opened by zhutiansheng over 4 years ago - 1 comment

#32 - no decoy in library

Issue - State: closed - Opened by zhutiansheng over 4 years ago - 1 comment

#31 - Fix decoding problem

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

#30 - implement cross validated smoothness parameter

Pull Request - State: closed - Opened by guoci over 4 years ago - 2 comments

#29 - correct typo

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

#28 - change default for `im_lowess_fraction`

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

#27 - use linear regression for small reference size

Pull Request - State: closed - Opened by guoci over 4 years ago - 1 comment

#26 - get basename without _(un)calibrated suffix, if any

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

#25 - bugfix for max_intensity == 0

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

#24 - bugfix match_modifications

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

#23 - bugfix to include more pepXML extensions.

Pull Request - State: closed - Opened by guoci over 4 years ago - 1 comment

#22 - Adaptation for idxml support

Pull Request - State: closed - Opened by Leon-Bichmann over 4 years ago - 5 comments

#21 - bugfix alignment plots

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

#20 - bugfix for non multi rank data

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

#19 - Feature/multi rank

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

#18 - Bugfix for modifications on AAs at N-term or C-term

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

#17 - Bugfix for modifications on AAs at N-term or C-term

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

#16 - restore `group_id` column, removed in 85f4a287beb3ea82a105d4bbfd39447…

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

#15 - Bugfix a TypeError

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

#14 - [FEATURE] make PyProphet an optional dependency

Pull Request - State: closed - Opened by guoci almost 5 years ago

#13 - [FEATURE] Support for MSFragger's calibrated MGF

Pull Request - State: closed - Opened by guoci almost 5 years ago - 1 comment

#12 - [FIX] bugfix for previous commit

Pull Request - State: closed - Opened by guoci almost 5 years ago

#11 - [FIX] Use unfiltered data when `psm.tsv` and `peptide.tsv` is used.

Pull Request - State: closed - Opened by guoci almost 5 years ago

#10 - Support search_hits with multiple same hit_ranks

Pull Request - State: closed - Opened by ppedrioli almost 5 years ago - 1 comment

#9 - Feature/separate rt im

Pull Request - State: closed - Opened by grosenberger about 5 years ago

GitHub / grosenberger/easypqp issues and pull requests