bigbio/quantms

Issues

• quantms-utils and mokapot error

  #377 opened a month ago by ypriverol
  0

• SDRF Parsing Error

  #376 opened a month ago by jackrogan
  1

• Moving bin scripts to library helper

  #375 opened a month ago by ypriverol
  0

• We should create a database for all the msgf+ jobs

  #367 opened 2 months ago by ypriverol
  1

• [BUG] Setting the `diann_speclib` to an empty string breaks the pipeline

  #372 opened 2 months ago by jspaezp
  3

• Comet new version has been released Comet v2024.01.0

  #371 opened 2 months ago by ypriverol
  2

• Option to skip mzml conversion

  #370 opened 2 months ago by sooheon
  1

• Unknown AA in peptide sequence compute MonoIsotopic Mass

  #368 opened 2 months ago by ypriverol
  18

• quantms failing with a big dataset 15K files

  #339 opened 2 months ago by ypriverol
  6

• Defining more enzymes in OpenMS Comet adaptor

  #354 opened 4 months ago by ypriverol
  9

• the charge min and max and missclevages are sometimes not working

  #364 opened 3 months ago by ypriverol
  3

• Identification workflow needed.

  #346 opened 3 months ago by ypriverol
  0

• USI reported by quantms for DIANN experiments.

  #350 opened 5 months ago by ypriverol
  27

• DIA-NN - automated handling of challenging data

  #330 opened 6 months ago by michaelsteidel86
  2

• quantms update figure of SVG pipeline.

  #347 opened 5 months ago by ypriverol
  0

• Test the impact and how the parameter num_hits works

  #344 opened 5 months ago by ypriverol
  4

• Open-search with quantms, use cases and workflow

  #345 opened 5 months ago by ypriverol
  1

• Big datasets more than 200 GB mztab size are not supported.

  #342 opened 6 months ago by ypriverol
  0

• Bug with ConsensusID

  #343 opened 6 months ago by ypriverol
  8

• Support for Phosphoproteomics datasets.

  #334 opened 6 months ago by ypriverol
  0

• Benchmark skip pre-analysis vs full preanalysis.

  #338 opened 6 months ago by ypriverol
  2

• We should dynamically configure some of the steps depending of the experiment size.

  #340 opened 6 months ago by ypriverol
  2

• Improve the skip pre-analysis parameter logic

  #337 opened 6 months ago by ypriverol
  2

• Phospho data for the CI/CD is missing

  #336 opened 6 months ago by ypriverol
  3

• mztab exporter failing for big dataset `PXD030304`

  #323 opened 6 months ago by ypriverol
  1

• LFQ MBR FDR algorithm needed.

  #303 opened 9 months ago by ypriverol
  8

• DIA-NN convert to mzTab failing

  #333 opened 6 months ago by ypriverol
  1

• Warning message should be removed

  #322 opened 6 months ago by ypriverol
  0

• SAGE jobs are not caching

  #326 opened 6 months ago by ypriverol
  1

• Plasma data LFQ failing

  #332 opened 6 months ago by ypriverol
  1

• Error converting to diann to mztab

  #328 opened 6 months ago by ypriverol
  3

• SAGE error in Big dataset TMT

  #329 opened 7 months ago by ypriverol
  11

• SAGE failing in big database

  #327 opened 7 months ago by ypriverol
  13

• Bug with mzTab export in single cell dataset

  #318 opened 8 months ago by ypriverol
  3

• Bug mzTab export in TMT dataset

  #320 opened 8 months ago by ypriverol
  9

• While testing the last release of OpenMS found again problem with MSGF+

  #315 opened 8 months ago by ypriverol
  1

• analysis of DIA runs fails

  #311 opened 8 months ago by jayieh
  4

• Reports of quantms into tower

  #309 opened 8 months ago by ypriverol
  0

• proteomicsLFQ with new SVM results in UPS1 dataset

  #301 opened 9 months ago by ypriverol
  23

• Bug in SAGE

  #298 opened 9 months ago by ypriverol
  1

• SAGE error with modification not supported

  #285 opened 9 months ago by ypriverol
  8

• Single cell analysis performance with worse results

  #287 opened 9 months ago by daichengxin
  69

• TMT ProteinInference bug with SAGE

  #299 opened 9 months ago by ypriverol
  1

• SAGE bug with Percolator

  #286 opened 9 months ago by ypriverol
  20

• Strange issue with SAGE

  #296 opened 9 months ago by ypriverol
  5

• SAGE search engine score is missing after psm re-scoring using percolator

  #288 opened 9 months ago by WangHong007
  22

• Remove references to PTXQC

  #290 opened 9 months ago by ypriverol
  1

• Another quantms MSstats error

  #282 opened 10 months ago by ypriverol
  1

• More parameters for MSstats

  #283 opened 10 months ago by ypriverol
  0

• Bug with msstats and quantms

  #280 opened 10 months ago by ypriverol
  0