Issues

• DecouplR provides a variety of enrichment tools with a cleaner implementation

  enhancement
  EngreitzLab/gene_network_evaluation#64 · Filter by author aron0093 opened on Jul 21, 2025
  

• Ensure consistency of multiple test correction methods

  EngreitzLab/gene_network_evaluation#50 · Filter by author adamklie opened on Sep 12, 2024

• Fix: categorical association dataframe output

  bugdashboardenhancementevaluations
  EngreitzLab/gene_network_evaluation#46 · Filter by author aron0093 opened on Sep 9, 2024 · 2024 Gene Program Jamboree
  3

  

• Code maintenance and good practices

  enhancement
  EngreitzLab/gene_network_evaluation#41 · Filter by author aron0093 opened on Sep 5, 2024

• Add an evaluation for model robustness

  discussionenhancement
  EngreitzLab/gene_network_evaluation#36 · Filter by author aron0093 opened on Sep 5, 2024

• Expose motif match significance threshold to users for motif enrichment

  enhancement
  EngreitzLab/gene_network_evaluation#34 · Filter by author aron0093 opened on Sep 5, 2024 · 2024 Gene Program Jamboree
  1

  

• Add support for perturbation association tests stratified per categorical level

  enhancementevaluations
  EngreitzLab/gene_network_evaluation#33 · Filter by author aron0093 opened on Sep 5, 2024 · 2024 Gene Program Jamboree
  2

  

• Calibration of association tests

  dashboardenhancement
  EngreitzLab/gene_network_evaluation#32 · Filter by author aron0093 opened on Sep 5, 2024
  

• General procedure to assess goodness of fit rather than explained variance ratio.

  discussionenhancement
  EngreitzLab/gene_network_evaluation#31 · Filter by author aron0093 opened on Sep 5, 2024

• Update gene set enrichment functionality

  enhancementevaluations
  EngreitzLab/gene_network_evaluation#29 · Filter by author adamklie opened on Aug 22, 2024 · 2024 Gene Program Jamboree
  3

  

• GSEA plot for individual program / term enrichment

  dashboarddiscussionenhancement
  EngreitzLab/gene_network_evaluation#28 · Filter by author adamklie opened on Aug 21, 2024

• Align dashboard with config from evaluation pipeline

  dashboardenhancement
  EngreitzLab/gene_network_evaluation#27 · Filter by author adamklie opened on Aug 21, 2024 · 2024 Gene Program Jamboree
  

• Trait enrichment results should be processed in evaluations

  enhancementevaluations
  EngreitzLab/gene_network_evaluation#26 · Filter by author adamklie opened on Aug 21, 2024 · 2024 Gene Program Jamboree
  1

  

• Structure plot

  dashboarddiscussionenhancement
  EngreitzLab/gene_network_evaluation#24 · Filter by author adamklie opened on Aug 21, 2024

• How are we handling promoter vs enhancer motif outputs from evaluation?

  dashboardenhancementquestion
  EngreitzLab/gene_network_evaluation#21 · Filter by author adamklie opened on Aug 21, 2024 · 2024 Gene Program Jamboree
  4

  

• Adding package versions to outputs from evaluation and (potentially) inference

  enhancement
  EngreitzLab/gene_network_evaluation#20 · Filter by author adamklie opened on Aug 21, 2024 · 2024 Gene Program Jamboree