Issues

• caretMultimodal failure on run fold model for simuldated data with dt = 0, rho = 0.5

  CompBio-Lab/MESSI-pipeline#109 · Filter by author tonyliang19 opened on Feb 26, 2026
  1

• Replace subworkflow/helpers.nf print_parameters to programatically log params

  CompBio-Lab/MESSI-pipeline#101 · Filter by author tonyliang19 opened on Jan 20, 2026

• Update doc in how to add a method as part of the MESSI pipeline

  CompBio-Lab/MESSI-pipeline#99 · Filter by author tonyliang19 opened on Jan 20, 2026
  

• Add caretMultimodal as part of the pipeline

  CompBio-Lab/MESSI-pipeline#98 · Filter by author tonyliang19 opened on Jan 20, 2026

• DIABLO-full design on thca and brca dataset gives zero devision warning, since only having predicted one label due to low predicted probability

  CompBio-Lab/MESSI-pipeline#77 · Filter by author tonyliang19 opened on Aug 4, 2024

• Some improvements to address for current pipeline

  enhancement
  CompBio-Lab/MESSI-pipeline#75 · Filter by author tonyliang19 opened on Jul 31, 2024

• Not clear data preprocessing on handling different types of omics data

  CompBio-Lab/MESSI-pipeline#74 · Filter by author tonyliang19 opened on Jul 31, 2024

• Creating MultiAssayExperiment with experiments and colData matching criteria

  CompBio-Lab/MESSI-pipeline#72 · Filter by author tonyliang19 opened on Jul 19, 2024

• Adding method from template is not stable at this moment?

  CompBio-Lab/MESSI-pipeline#70 · Filter by author tonyliang19 opened on Jul 12, 2024

• To add new method, need to first load conda or pip to have deps ready

  Project Setup
  CompBio-Lab/MESSI-pipeline#68 · Filter by author tonyliang19 opened on Jul 10, 2024

• Add manual time snapshotting in select feature logic

  CompBio-Lab/MESSI-pipeline#67 · Filter by author tonyliang19 opened on Jul 5, 2024

• Potential datasets

  CompBio-Lab/MESSI-pipeline#65 · Filter by author tonyliang19 opened on Jul 3, 2024

• paramsSummaryLog is not stable and only works with the NOT *-all binary

  bugProject Setup
  CompBio-Lab/MESSI-pipeline#62 · Filter by author tonyliang19 opened on Jul 3, 2024

• Poster / Figures todos

  documentation
  CompBio-Lab/MESSI-pipeline#60 · Filter by author tonyliang19 opened on Jul 3, 2024

• Useful utilities todos

  documentation
  CompBio-Lab/MESSI-pipeline#59 · Filter by author tonyliang19 opened on Jul 3, 2024
  3

• Feature selection todos

  documentation
  CompBio-Lab/MESSI-pipeline#58 · Filter by author tonyliang19 opened on Jul 3, 2024

• Cross validation todos

  documentation
  CompBio-Lab/MESSI-pipeline#57 · Filter by author tonyliang19 opened on Jul 3, 2024

• Project Setup (apptainer, remote, etc) todos

  documentation
  CompBio-Lab/MESSI-pipeline#56 · Filter by author tonyliang19 opened on Jul 3, 2024

• Prepare data todos

  documentation
  CompBio-Lab/MESSI-pipeline#54 · Filter by author tonyliang19 opened on Jul 3, 2024

• Simplify method related process to withName: matching regex for declaring container

  Project Setup
  CompBio-Lab/MESSI-pipeline#52 · Filter by author tonyliang19 opened on Jun 26, 2024

• Standardize step of method feature selection process

  CompBio-Lab/MESSI-pipeline#9 · Filter by author tonyliang19 opened on Jun 18, 2024

• Handle uncompress when tar.gz only contains one h5mu or mae_data

  CompBio-Lab/MESSI-pipeline#12 · Filter by author tonyliang19 opened on Jun 18, 2024

• Methods to look into

  CompBio-Lab/MESSI-pipeline#15 · Filter by author tonyliang19 opened on Apr 2, 2024
  1

• Ongoing TODO list, PINNED, linking to other issues

  documentation
  CompBio-Lab/MESSI-pipeline#16 · Filter by author tonyliang19 opened on Apr 2, 2024
  3

  

• Convert MuData and MAE easily

  CompBio-Lab/MESSI-pipeline#18 · Filter by author tonyliang19 opened on Feb 23, 2024
  1