saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells

saeyslab/nichenetr Issues

Parallelization error when optimizing parameters for NicheNet
Updated a month ago4
Low AUPR values in analyses
Updated a month ago3
discrepancy in results output
Updated a month ago
Change error in `alias_to_symbol_seurat()` to warning
Closed a month ago
Naming convention in prioritization table
Updated a month ago
Error in WhichCells.Seurat(object = object, idents = ident.2) : Cannot find the following identities in the object: Adjacent
Closed a month ago1
when sender cell type is only one,
Updated a month ago1
there is a warning in this shetp-"score ligand-receptor interactions based on expression strength of the receptor"
Closed a month ago
Protein complex
Updated a month ago1
Receiver cells in differential analysis
Closed a month ago1
Condition_colname is not used for subsetting in nichenet_seuratobj_aggregate
Closed a month ago2
How is the Ligand-Target-Matrix generated?
Updated a month ago2
Only activating interactions or also repressing?
Closed a month ago1
Can NicheNet be used for analyzing three groups?
Updated a month ago1
Different results running. the same. code in different version. of
Closed a month ago6
Error when passing the recorrect_umi argument in get_lfc_celltype
Closed a month ago1
Function generate_info_tables return an error
Closed 2 months ago3
Error in `Idents<-`: ! 'value' must be a factor or vector
Updated 2 months ago3
RankActiveLigands Error
Closed 2 months ago
How should I assign a pathway/pathways to the target genes when running nichenetr?
Closed 3 months ago3
how to use nichenet in cell development data
Closed 4 months ago4
How exactly the ligand activity were calculate?
Closed 4 months ago1
`generate_prioritization_tables` warnings and documentation
Updated 4 months ago
Warning message in `predict_ligand_activities`
Updated 4 months ago
Error in `generate_info_tables`
Closed 4 months ago
`assign_ligands_to_celltype` bug when there are no general ligands
Closed 4 months ago
`get_exprs_avg` changes underscore to hyphen in cell type names
Closed 4 months ago
cannot complete assign_ligands_to_celltype
Closed 4 months ago2
`make_line_plot` bugs
Closed 4 months ago
what is ligand_tf_matrix for??
Closed 4 months ago1
Preferable metric to infer cell-to-cell communication
Closed 4 months ago1
I can't install nichenet
Closed 4 months ago1
missing function for circos plot visualization
Closed 5 months ago2
Query: AUPR
Closed 5 months ago1
I cannot run the "get_weighted_ligand_receptor_links" and "prepare_ligand_receptor_visualization" while I have nichnetr installed
Closed 5 months ago2
How to choose the best ligand to continue analysis with the potential ligand?
Updated 5 months ago
SeuratV5
Closed 5 months ago4
Error running nichenet_seuratobj_aggregate on v5 Seurat obj
Closed 5 months ago7
Error finding log fold change information of ligands from sender cells (Seurat V5 object)
Closed 5 months ago6
Zenodo Data Inquiry
Closed 6 months ago1
Inquiry about Signaling and Gene Regulatory Networks Data in Omnipath and NicheNet
Closed 6 months ago1
Assistance Needed: nichenetr Package Installation Error in R
Closed 7 months ago
Identifying bonafide ligand-receptor pairs in the updated ligand-receptor database (V2)
Updated 7 months ago
Error while plotting a ligand-receptor interaction network
Updated 8 months ago
Error while running get_expressed_genes
Closed 8 months ago5
Is there a helper function to draw the plot in the description ?
Closed 8 months ago1
Modeling Inquiry
Closed 8 months ago2
Error in "evaluate_target_prediction(setting, ligand_target_matrix, ligands_position) : all genes have same response"
Updated 9 months ago
So much targets in nichenet_output$ligand_activity_target_heatmap after running nichenet_seuratobj_aggregate
Closed 9 months ago1
Error on get_prioritization_tables()
Closed 9 months ago1