compomics/DeepLC

Issues

• Documentation or reference for missing models

  #78 opened a month ago by vrkosk
  2

• Datasets

  #77 opened a month ago by xiaosiruwei
  1

• Tons of warnings when using iTRAQ4plex or iTRAQ8plex

  #75 opened 2 months ago by vrkosk
  3

• Take Unimod modification compositions from psims.controlled_vocabulary.unimod

  #76 opened 2 months ago by vrkosk
  2

• Cholesky AttributeError from DeepLC fix by down versioning to scikit-learn==1.3.2, scipy==1.11.4

  #74 opened 2 months ago by KarlClauser
  1

• Documentation: table of peptide properties of training data sets

  #73 opened 3 months ago by vrkosk
  2

• GUI DeepLC errors

  #71 opened 5 months ago by MassambaNdiaye
  3

• data set

  #70 opened 6 months ago by HR-RH
  0

• pip install on Python 3.10 not working correctly

  #39 opened 3 years ago by levitsky
  9

• How can I get the PSI-MS format for the 'modifications' column?

  #67 opened 10 months ago by ec-ho-ra-mos
  12

• How is it possible to predict RT when DeepLC doesnt know the LC gradient

  #66 opened 10 months ago by candidaorelmex
  4

• How to configure support for selenocysteine in its carbamidomethylated form?

  #62 opened a year ago by KarlClauser
  2

• Possibility to retrain a model

  #12 opened 4 years ago by cctsou
  1

• Training new models

  #63 opened a year ago by KarlClauser
  3

• batch_num is not used anymore in the resent versions

  #58 opened a year ago by markmipt
  3

• Pygam calibration is the only option in the latest version

  #59 opened a year ago by markmipt
  5

• deeplc gui

  #57 opened a year ago by HR-RH
  4

• Error during calibration using modified peptides

  #56 opened a year ago by steffenlem
  4

• I cannot run it on website when my file getting bigger

  #55 opened a year ago by hetaofan
  2

• Low prediction accuracy for versions 2.0.4+

  #54 opened a year ago by markmipt
  3

• error using GUI to predict rt

  #53 opened a year ago by sehooni
  3

• How to convert peptide modifications of maxquant output file to MS2PIP-style

  #44 opened 2 years ago by lbwfff
  5

• Error when using unmodified peptide to train and using modified peptides to test

  #48 opened 2 years ago by WeiqiangChen
  7

• error using https://iomics.ugent.be/deeplc/

  #46 opened 2 years ago by WeiqiangChen
  3

• The last of default models is selected as the best one

  #40 opened 2 years ago by caetera
  4

• scikit-learn / sklearn missing from dependency list

  #37 opened 3 years ago by RalfG
  2

• Deeplc docker GPU support

  #36 opened 3 years ago by Hendricks27
  2

• negative retention times

  #34 opened 3 years ago by Seb-Leb
  4

• Predictions are slow when library is not full

  #31 opened 3 years ago by markmipt
  3

• What is the unit of tr: retention time (only required for calibration)?

  #21 opened 3 years ago by chinmayaNK22
  2

• DeepLC CPU vs GPU performance

  #20 opened 3 years ago by markmipt
  5

• DeepLC (tensorflow) does not seem to obey num_jobs

  #19 opened 4 years ago by RalfG
  2

• Bioconda package autobump has some issues

  #17 opened 4 years ago by RalfG
  1

• DeepLC as a docker image

  #16 opened 4 years ago by MarcIsak
  2

• Skipping calibration step?

  #14 opened 4 years ago by MarcIsak
  4

• Raise `TypeError: object of type 'float' has no len()` for the table without modifications

  #15 opened 4 years ago by DongElkan
  0

• DeepLC 0.1.14 crashes my computer systematically when a peptide file for calibration is not supplied

  #11 opened 4 years ago by MarcIsak
  2

• Python 3.8 compatibility

  #9 opened 4 years ago by paretje
  3

• Blank spot after calibration

  #10 opened 4 years ago by courcelm
  8