wilhelm-lab/oktoberfest

Issues

• Question regarding the numThreads parameter

  #303 opened 16 days ago by mhamaneh
  1

• Docs: Clean module docs for `predict` module

  #267 opened 15 days ago by JSchlensok
  0

• Local prediction: Clean progress bar for multi-threaded prediction

  #266 opened 3 months ago by JSchlensok
  0

• Better hint on failure to connect to public koina instance

  #175 opened 3 months ago by picciama
  1

• Mokapot and percolator error MSfragger pepxml.

  #131 opened 3 months ago by Skourtis
  3

• Finish the pipeline: Add pickedGroupFDR for quantification

  #164 opened 3 months ago by picciama
  0

• Summary report

  #262 opened 3 months ago by picciama
  0

• Refinement learning: RT prediction

  #261 opened 3 months ago by picciama
  0

• Refinement learning: Ce calibration

  #260 opened 3 months ago by picciama
  0

• Make use of matched peak information from Sage

  #244 opened 5 months ago by picciama
  0

• Better description on how to install external dependencies

  #132 opened a year ago by karimwh
  0

• Fail / warn if no spectra files are found

  #169 opened a year ago by picciama
  0

• Rescoring the Sage output doesn't work

  #211 opened 6 months ago by GiammaFer75
  2

• Oktoberfest crashes with Error message "could not find any target"

  #255 opened 4 months ago by mhamaneh
  14

• Additional percolator/mokapot features for custom file input

  #233 opened 4 months ago by ChrisMcGann
  5

• Missing proteins column when using internal format for spectral library generation

  #253 opened 4 months ago by picciama
  0

• ERROR - spectrum_io.file.hdf5::write_dataset value too large to convert to int

  #199 opened 5 months ago by colin986
  3

• The model is not known

  #216 opened 5 months ago by tobiasko
  15

• Missing ProteinID in the generated Spectral Lib and timsTOF questions

  #238 opened 5 months ago by TotoroCat1
  14

• --version

  #228 opened 5 months ago by tobiasko
  1

• Fallback mechanism needed if retention time alignment fails

  #159 opened 5 months ago by MatthewThe
  3

• Supporting multiple PSM rank for rescoring

  #118 opened a year ago by arminsl
  1

• Prosit Website Typo

  #157 opened a year ago by CCranney
  8

• InferenceServerException: [StatusCode.UNKNOWN] Stream removed

  #174 opened 10 months ago by colin986
  6

• Does Oktoberfest already support Prosit_2023_intensity_TOF?

  #136 opened 10 months ago by tobiasko
  6

• How to define CE and charge state for spectral library generation workflow

  #126 opened 10 months ago by tobiasko
  7

• [UI] Upload multiple files

  #193 opened a year ago by WassimG
  0

• [UI] Fix config file generated by Vue

  #181 opened a year ago by WassimG
  0

• [UI] [Flask] Get number of pending tasks

  #192 opened a year ago by WassimG
  0

• [Flask] Number of Running jobs

  #184 opened a year ago by WassimG
  0

• [UI] Specify koina url

  #186 opened a year ago by WassimG
  0

• [Flask] Return proper error message

  #191 opened a year ago by WassimG
  0

• [Database] Create a proper table for logging

  #190 opened a year ago by WassimG
  0

• [Pipeline] Create a cleanup daemon

  #189 opened a year ago by WassimG
  0

• Write Documentaion

  #183 opened a year ago by WassimG
  0

• [UI] Add Miscelaneous optional config properties

  #188 opened a year ago by WassimG
  0

• [UI] Add fasta digest to UI

  #187 opened a year ago by WassimG
  0

• Write Unit tests

  #185 opened a year ago by WassimG
  0

• Create startup script

  #182 opened a year ago by WassimG
  0

• streamlining option: config parameter "library_input_type" is not required

  #179 opened a year ago by ayla-s
  0

• CE calibrating FragPipe results generated from mzML formatted data fails

  #129 opened a year ago by tobiasko
  45

• Percolator returns error in Rescoring "CalledProcessError: Command 'percolator --weights..."

  #151 opened a year ago by RicZenChioz
  2

• Pyteomics pepXML reader mislabel targets and decoys

  #154 opened a year ago by WassimG
  0

• FileNotFoundError: [Errno 2] No such file or directory: when running Spectral library generation

  #147 opened a year ago by RicZenChioz
  2

• add log file and copy of paramter to output directory

  #130 opened a year ago by tobiasko
  2

• minimalistic config files for all workflows

  #128 opened a year ago by tobiasko
  4

• in silico digestion ignores cleavage setting

  #127 opened a year ago by tobiasko
  2

• Optimize raw file reading for CE calibration only

  #135 opened a year ago by picciama
  0

• File exists error mzml input

  #124 opened a year ago by patrick-willems
  4

• tmtpro flag only adds tag to lysines, not n-term.

  #123 opened a year ago by ChrisMcGann
  2