PyProphet/pyprophet issues and pull requests

#128 - Patch/export parquet

Pull Request - State: closed - Opened by jcharkow 5 days ago

#127 - Update Report with PP plot

Pull Request - State: closed - Opened by singjc 24 days ago

#126 - Feature/speedup parquet export

Pull Request - State: closed - Opened by jcharkow 26 days ago - 4 comments

#125 - singularity pull issue

Issue - State: open - Opened by HFan11 4 months ago - 6 comments

#124 - pip install fails claiming that numpy is not installed

Issue - State: open - Opened by kometkamerat 7 months ago - 6 comments

#123 - Feature/split

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

#122 - [ADD] peptide sequence specific filtering for sqMass and OSW filtering

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

#121 - [FIX] deprecation warning with pandas

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

#120 - Metabolomics - Global Context

Issue - State: open - Opened by bruadi over 1 year ago

#119 - sqlite3.OperationalError:database is locked

Issue - State: open - Opened by yuz2011 over 1 year ago - 3 comments

#118 - Fix broken osw tests and report/deprecation warnings

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

#117 - [FEATURE] add feature names to xgboost output

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

#116 - AssertionError: Column group_id is not in input file(s).

Issue - State: open - Opened by ajsweatt over 1 year ago - 1 comment

#115 - Fix/ipf np int

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

#114 - Update/main score selection

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

#113 - Fix/apply weights

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

#112 - [FIX] PyPDF2 3.0.0 deprecation of PdfFileMerger, PdfFileReader to Pdf…

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

#111 - Parquet Export

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

#110 - Feature/dynamic main score

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

#109 - [MINOR] Docker file end bind mount point

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

#108 - Feature/filter osw

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

#107 - [MINOR] Add exception handling for when applying weights and not spec…

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

#106 - Exception handling when applying weights

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

#105 - sqlite3.OperationalError: no such table: PYPROPHET_WEIGHTS

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

#104 - How can I calculate the sub score?

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

#103 - [ADD] Add pi0estimation extended error help into separate PR from PR …

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

#102 - [FEATURE] Separate color blind friendly feature into separate PR from …

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

#101 - Fix IPF Export with Unimod to Codename Table

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

#100 - Allow for color adjustment of the automatically generated target decoy plots

Issue - State: closed - Opened by Matthias313 almost 3 years ago

#99 - nearly identical pep/qvalue distribution for target and decoy but with bimodal distribution on score

Issue - State: closed - Opened by kairenchen721 about 3 years ago - 7 comments

#98 - sqlite3.Integrity Error

Issue - State: closed - Opened by fangfeiz over 3 years ago - 17 comments

#97 - error of using pyprophet-cli

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

#96 - Remove m_score filtering?

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

#95 - [FIX] Cython in setup.py / Include PYX

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

#94 - Fix/cython

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

#93 - [RELEASE] PyProphet 2.1.8

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

#92 - _optimize.pyx missing from tarball on pypi

Issue - State: closed - Opened by dpryan79 over 3 years ago - 2 comments

#91 - [FIX] Cython build in setup.py

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

#90 - [FIX] Report only targets in overview report

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

#89 - Decoys peptides are counted in pyprophet statistics

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

#88 - pyprophet ipf error

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

#87 - ADD: export before scoring with MS1MS2 scores

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

#86 - Issue Module Import py.test

Issue - State: open - Opened by oliveralka over 4 years ago

#85 - merge step fails with `sqlite3.OperationalError: table FEATURE has 3 columns but 9 values were supplied`

Issue - State: closed - Opened by cbielow over 4 years ago - 2 comments

#84 - OpenSWATH IPF workflow errored.

Issue - State: closed - Opened by andyzim111 over 4 years ago - 2 comments

#83 - [ADD] ScoreFilter

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

#82 - Feature/merged subsampling

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

#81 - [FIX] Minor patches & Release 2.1.5

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

#80 - [FEATURE] IPF reading speedup & first version of statistics report

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

#79 - Revert "Export compounds scored on ms1 level (SCORE_MS1)"

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

#78 - pi0 in legacy code

Issue - State: closed - Opened by mantouRobot almost 5 years ago - 2 comments

#77 - Error: At least 10 decoy groups and 10 target groups are required

Issue - State: closed - Opened by lmangnier almost 5 years ago - 4 comments

#76 - [RELEASE] Version 2.1.4

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

#75 - Export compounds scored on ms1 level (SCORE_MS1)

Pull Request - State: closed - Opened by oliveralka almost 5 years ago - 7 comments

#74 - Note: Installing xgboost on MacOS Catalina 10.15 (pyprophet)

Issue - State: closed - Opened by oliveralka about 5 years ago - 1 comment

#73 - Assay RT calculation is not proper

Issue - State: open - Opened by shubham1637 about 5 years ago - 7 comments

#72 - Merging across different libraries

Issue - State: open - Opened by hroest about 5 years ago

#71 - Question about calculating scores based the LDA scalings_

Issue - State: closed - Opened by mantouRobot about 5 years ago - 6 comments

#70 - ImportError: cannot import name 'factorial'

Issue - State: closed - Opened by fangfeiz about 5 years ago

#69 - [FIX] Reduced merging patch

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

#68 - [FEATURE] Speedup for merging

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

#67 - [FIX] Updated regression tests for dependencies

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

#66 - [FIX] merge osw with compounds

Pull Request - State: closed - Opened by oliveralka over 5 years ago - 1 comment

#65 - pyprophet export ends w/o any output

Issue - State: closed - Opened by mwalzer over 5 years ago - 4 comments

#64 - [FEATURE] allow gene-level scoring

Pull Request - State: closed - Opened by hroest over 5 years ago - 1 comment