Issues

• network_graph ! vertices contains duplicated vertex names

  saeyslab/multinichenetr#128 · Filter by author annaborchers opened on May 23, 2026

• make_ligand_activity_target_plot fails when only one ligand is selected

  saeyslab/multinichenetr#127 · Filter by author KurayiChawatama opened on May 20, 2026

• Typo In "MultiNicheNet analysis: MIS-C threewise comparison - step-by-step" Vignette

  saeyslab/multinichenetr#126 · Filter by author KurayiChawatama opened on May 14, 2026

• Deprecation Warnings From S4Vectors:::anyMissing()

  saeyslab/multinichenetr#125 · Filter by author KurayiChawatama opened on May 13, 2026

• Prioritization based only on ligand activity (ignoring ligand/receptor expression) in MultiNicheNet

  saeyslab/multinichenetr#124 · Filter by author donghyeon321 opened on Apr 20, 2026
  2

• Regarding dependency package version issues

  saeyslab/multinichenetr#123 · Filter by author PanSX-Dr opened on Dec 24, 2025

• Error in get_DE_info when including batch as batch or covariate after F7-only subsetting

  saeyslab/multinichenetr#120 · Filter by author nourmh11 opened on Nov 19, 2025

• Renaming input dataset (column name issue) and pseudobulk analysis output

  saeyslab/multinichenetr#119 · Filter by author jasoncrucify opened on Oct 31, 2025

• Looking for support to make Differential intercellular Signaling Cascade between cell types with multinichenet

  saeyslab/multinichenetr#118 · Filter by author Bioanya opened on Oct 28, 2025

• Looking for Support with the correct vignette to follow / contrast setting

  saeyslab/multinichenetr#117 · Filter by author Smeerlap opened on Oct 2, 2025

• Change weights in favor of LR expression

  enhancement
  saeyslab/multinichenetr#101 · Filter by author CDSchuster opened on Dec 5, 2024
  3

• make_sample_lr_prod_activity_plots_Omnipath Has No Obvious Ordering

  documentation
  saeyslab/multinichenetr#93 · Filter by author DarioS opened on Sep 25, 2024
  1

• Gene Pairs Below Threshold Appear in Plot

  bugdocumentationenhancement
  saeyslab/multinichenetr#92 · Filter by author DarioS opened on Sep 19, 2024
  2

• ligand_target_matrix Creation Needs Copying and Pasting of Large Chunk from Vignette

  enhancement
  saeyslab/multinichenetr#90 · Filter by author DarioS opened on Sep 9, 2024

• Inability to Compactly Plot Multiple Phenotypes

  enhancement
  saeyslab/multinichenetr#89 · Filter by author DarioS opened on Aug 29, 2024
  2

• Redundant Comparison Shown

  enhancement
  saeyslab/multinichenetr#84 · Filter by author DarioS opened on Aug 9, 2024
  2

• combine_sender_receiver_de Duplicate Function Causes Error

  documentationenhancement
  saeyslab/multinichenetr#74 · Filter by author DarioS opened on Jun 17, 2024

• Potential namespace conflict with the summarise function

  documentationenhancement
  saeyslab/multinichenetr#73 · Filter by author Huangy57 opened on Jun 12, 2024

• How to manually adjust legend in make_sample_lr_prod_activity_plots()?

  enhancement
  saeyslab/multinichenetr#30 · Filter by author VivianQM opened on Sep 8, 2023
  1

• Issue with parallelization of get_ligand_activities_targets_DEgenes on some systems

  bug
  saeyslab/multinichenetr#20 · Filter by author browaeysrobin opened on Aug 10, 2023
  5