lehtiolab/ddamsproteomics

Issues

• QC improvements

  #28 opened a year ago by glormph
  1

• Add some metrics to PSM table

  #36 opened 5 months ago by glormph
  0

• sampletable order is important in DEqMS

  #33 opened a year ago by glormph
  0

• Add `-Xmx` to dinosaur process to increase heap size

  #30 opened a year ago by glormph
  0

• Setnames/groupnames cannot be too similar for then the "add sample group to header" regex fails

  #31 opened a year ago by glormph
  1

• msgf2pin does not use not all PSMs in a run

  #27 opened a year ago by glormph
  1

• make possible to exclude specific channels for summarized quant

  #29 opened a year ago by glormph
  0

• Create formalized tests

  #22 opened 2 years ago by glormph
  1

• Create user-defined column(s) with flags for occurance of particular protein type, contaminant etc

  #5 opened a year ago by glormph
  0

• Unify pgt and dda mzmldef

  #24 opened a year ago by glormph
  0

• Enforce concatenated search for percolator

  #26 opened a year ago by glormph
  0

• Make possible to accept correction matrix for isobaric quant

  #25 opened 2 years ago by glormph
  1

• setname mismatch between total proteome/PTM search should be reported as error

  #23 opened 2 years ago by glormph
  0

• Removal of target-matching decoy peptides skews database

  #19 opened 2 years ago by glormph
  1

• off by one error in PTM protein location

  #17 opened 2 years ago by glormph
  0

• Add tmt18 pro when openms has it

  #14 opened 2 years ago by glormph
  0

• Isobaric prec.purity calc for TIMS needs newer pwiz version

  #6 opened 2 years ago by glormph
  0

• Investigate and document difference PTM and peptide tables

  #9 opened 2 years ago by glormph
  1

• Update status code for retries

  #10 opened 2 years ago by glormph
  0

• Pipeline reruns crash on file exists (trace)

  #12 opened 2 years ago by glormph
  0

• Investigate and document missing sets in PTM peptide table

  #7 opened 2 years ago by glormph
  1

• Investigate and document PTM peptides / peptides dis

  #8 opened 2 years ago by glormph
  1

• docker hub shutdown - use biocontainers instead

  #13 opened 2 years ago by glormph
  2

• setMerge doesnt cache on resume

  #11 opened 2 years ago by glormph
  0