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saeyslab
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nichenetr
NicheNet: predict active ligand-target links between interacting cells
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Error when passing the recorrect_umi argument in get_lfc_celltype
#282
NeuralBind
opened
3 weeks ago
1
`generate_prioritization_tables` warnings and documentation
#281
csangara
opened
1 month ago
0
Warning message in `predict_ligand_activities`
#280
csangara
opened
1 month ago
0
Fix bug in `generate_info_tables`
#279
csangara
closed
1 month ago
0
Error in `generate_info_tables`
#278
csangara
closed
1 month ago
0
Fixes `assign_ligands_to_celltype` when there are no general ligands
#277
csangara
closed
1 month ago
0
`assign_ligands_to_celltype` bug when there are no general ligands
#276
csangara
closed
1 month ago
0
Fix bugs in `assign_ligands_to_celltype`
#275
csangara
closed
1 month ago
0
Added checks for `get_exprs_avg` in case cell type names have an underscore
#274
csangara
closed
1 month ago
0
Fixed `make_line_plot` bugs
#273
csangara
closed
1 month ago
0
`make_line_plot` bugs
#272
csangara
closed
1 month ago
0
Condition_colname is not used for subsetting in nichenet_seuratobj_aggregate
#271
singlecellfan
opened
1 month ago
2
I can't install nichenet
#270
panchen007
closed
1 month ago
1
missing function for circos plot visualization
#269
cklee7
closed
1 month ago
2
cannot complete assign_ligands_to_celltype
#268
shawnshu1
closed
1 month ago
2
How should I assign a pathway/pathways to the target genes when running nichenetr?
#267
pariaaliour
opened
1 month ago
3
How to choose the best ligand to continue analysis with the potential ligand?
#266
pariaaliour
opened
1 month ago
0
`get_exprs_avg` changes underscore to hyphen in cell type names
#265
csangara
closed
1 month ago
0
what is ligand_tf_matrix for??
#264
yuzzini
closed
1 month ago
1
Preferable metric to infer cell-to-cell communication
#263
JoshuaCumming
closed
1 month ago
1
I cannot run the "get_weighted_ligand_receptor_links" and "prepare_ligand_receptor_visualization" while I have nichnetr installed
#262
pariaaliour
closed
1 month ago
2
Version 2.1
#261
csangara
closed
2 months ago
0
How exactly the ligand activity were calculate?
#260
iceautumn
closed
4 weeks ago
1
Fixed wrapper function for Seurat v5 objects
#259
csangara
closed
3 months ago
0
Error finding log fold change information of ligands from sender cells (Seurat V5 object)
#258
niksa01
closed
2 months ago
6
SeuratV5
#257
shayansaniei
closed
2 months ago
4
Identifying bonafide ligand-receptor pairs in the updated ligand-receptor database (V2)
#256
alecorr
opened
4 months ago
0
Zenodo Data Inquiry
#255
xuansuyang
closed
2 months ago
1
Assistance Needed: nichenetr Package Installation Error in R
#254
ImtKhu
closed
3 months ago
0
Error running nichenet_seuratobj_aggregate on v5 Seurat obj
#253
DomenicoSkyWalker89
closed
2 months ago
7
Error while plotting a ligand-receptor interaction network
#252
Saumya513
opened
4 months ago
0
Query: AUPR
#251
nfancy
closed
1 month ago
1
`get_expressed_genes` - fix for Seurat v5 and add method for matrices
#250
csangara
closed
5 months ago
1
Inquiry about Signaling and Gene Regulatory Networks Data in Omnipath and NicheNet
#249
xuansuyang
closed
2 months ago
1
Unit testing
#248
csangara
closed
5 months ago
0
`get_expressed_genes` - fix for Seurat v5 and add method for matrices
#247
csangara
closed
5 months ago
2
Is there a helper function to draw the plot in the description ?
#246
kaizen89
closed
5 months ago
1
Error in "evaluate_target_prediction(setting, ligand_target_matrix, ligands_position) : all genes have same response"
#245
zcaiwei
opened
5 months ago
0
Modeling Inquiry
#244
xuansuyang
closed
5 months ago
2
So much targets in nichenet_output$ligand_activity_target_heatmap after running nichenet_seuratobj_aggregate
#243
Magetutor
closed
6 months ago
1
Error while running get_expressed_genes
#242
Samir1703
closed
5 months ago
5
Error on get_prioritization_tables()
#241
qxiong2
closed
6 months ago
1
there is a warning in this shetp-"score ligand-receptor interactions based on expression strength of the receptor"
#240
GGboy-Zzz
opened
7 months ago
0
how to use nichenet in cell development data
#239
GGboy-Zzz
closed
4 weeks ago
4
generate_prioritization_tables() generates an empty result.
#238
yoshiakiabe1018
closed
8 months ago
1
NicheNet-v2 data source collection and processing (OmniPath)?
#237
beigelk
closed
8 months ago
2
ask questions about model constructing
#236
xuansuyang
closed
8 months ago
2
I got trouble when running nichenet_seuratobj_aggregate()
#235
fishskywd
closed
5 months ago
1
Trouble with get_prioritization_tables
#234
pushpinder-bu
closed
5 months ago
1
get_exprs_avg produced error message
#233
wang2034
closed
5 months ago
1
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