Issues

• Sampling strategy for large scRNA-seq dataset with highly imbalanced cell type abundances in NicheNet analysis

  saeyslab/nichenetr#345 · Filter by author boluofen opened on Jul 6, 2026

• Question regarding NicheNet for bulk RNA-seq and CITE-seq integration on the same time

  saeyslab/nichenetr#344 · Filter by author nourelhoudabarhoumi opened on Jun 16, 2026

• error from installing nichenetr

  saeyslab/nichenetr#340 · Filter by author wang2034 opened on Jan 2, 2026
  

• Difference between targets and receivers

  saeyslab/nichenetr#339 · Filter by author bapoorva opened on Nov 13, 2025

• Inference of the Receptors for unknown Ligands

  saeyslab/nichenetr#337 · Filter by author dslv3y opened on Oct 20, 2025
  1

• error with nichenet_seuratobj_aggregate

  saeyslab/nichenetr#333 · Filter by author mvereten opened on Aug 10, 2025
  4

  

• convert_alias_to_symbol giving duplicate gene names

  saeyslab/nichenetr#331 · Filter by author annaborchers opened on Jul 16, 2025
  1

  

• How to compare multiple samples

  saeyslab/nichenetr#329 · Filter by author fightingevery opened on Jun 25, 2025

• Verschueren LR pairs directionality

  enhancement
  saeyslab/nichenetr#317 · Filter by author emmamoliere opened on Mar 7, 2025

• Ligand Target Signalling on bulk RNAseq datasets

  saeyslab/nichenetr#313 · Filter by author Shanthosh29 opened on Feb 5, 2025
  1

• "Error: None of the features provided found in this assay" when running nichenet_seuratobj_aggregate

  saeyslab/nichenetr#310 · Filter by author kangjiajinlong opened on Nov 26, 2024
  2

• DiffNicheNet for the same cell type in different time points?

  saeyslab/nichenetr#304 · Filter by author arunchakra opened on Sep 27, 2024

• assign_ligands_to_celltype erroe message

  bug
  saeyslab/nichenetr#303 · Filter by author wang2034 opened on Sep 13, 2024
  2

  

• Parallelization error when optimizing parameters for NicheNet

  saeyslab/nichenetr#292 · Filter by author tkapello opened on Aug 6, 2024
  4

• Error in Idents<-: ! 'value' must be a factor or vector

  saeyslab/nichenetr#284 · Filter by author XIANZHE-LI opened on Jul 13, 2024
  6

• generate_prioritization_tables warnings and documentation

  enhancement
  saeyslab/nichenetr#281 · Filter by author csangara opened on May 30, 2024

• Warning message in predict_ligand_activities

  enhancement
  saeyslab/nichenetr#280 · Filter by author csangara opened on May 30, 2024
  3

  

• How to choose the best ligand to continue analysis with the potential ligand?

  saeyslab/nichenetr#266 · Filter by author Paria06 opened on May 7, 2024

• Identifying bonafide ligand-receptor pairs in the updated ligand-receptor database (V2)

  saeyslab/nichenetr#256 · Filter by author alecorr opened on Mar 4, 2024
  1

• Error while plotting a ligand-receptor interaction network

  saeyslab/nichenetr#252 · Filter by author Saumya513 opened on Feb 10, 2024

• Error in "evaluate_target_prediction(setting, ligand_target_matrix, ligands_position) : all genes have same response"

  saeyslab/nichenetr#245 · Filter by author zcaiwei opened on Jan 9, 2024
  1

• make_ligand_activity_target_exprs_plot inconsistent ordering cell types

  saeyslab/nichenetr#142 · Filter by author browaeysrobin opened on May 11, 2022

• Seurat Wrapper + Circos visualization

  saeyslab/nichenetr#127 · Filter by author chrismahony opened on Feb 17, 2022
  1

• Conda package

  enhancement
  saeyslab/nichenetr#95 · Filter by author Zethson opened on Jul 23, 2021
  8

• nichenet through seurat-cell type specific ligand/receptor scores

  enhancement
  saeyslab/nichenetr#77 · Filter by author annamath opened on Mar 26, 2021
  4