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saeyslab
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multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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Use on multiple samples but no different conditions
#38
nvribeiro
closed
10 months ago
1
How to use bulk RNASeq data?
#37
akiss-me
closed
10 months ago
1
Dissecting direct vs indirect effects of simulation
#36
Git535323
closed
10 months ago
1
Interpretation of scaled ligand activity values
#35
carolinemorrell
closed
10 months ago
1
Fig 2b in preprint
#34
liaojinyue
closed
10 months ago
1
Interpreting raw and scaled ligand activity values
#33
noranekonobokkusu
closed
10 months ago
2
Condition-specific cell types - Can you run multinichenetr on datasets that have varying cell type composition?
#32
olympiahardy
closed
3 months ago
7
How to proceed when a cell type does not have enough number of cells in a group
#31
anemartinezlarrinaga2898
closed
11 months ago
1
How to manually adjust legend in make_sample_lr_prod_activity_plots()?
#30
VivianQM
opened
11 months ago
1
Error polygon edge not found for ggraph_signaling_path$plot
#29
lchan8
closed
9 months ago
2
DE analysis issue
#28
aokhan
closed
12 months ago
1
Error running multi_nichenet_analysis() in "Combine all the information in prioritization tables" step
#27
lchan8
closed
12 months ago
2
Setting multiple covariates and batches in multinichnet
#26
iichelhadi
closed
12 months ago
2
contrast table for 4 groups
#25
lw157
closed
12 months ago
4
Warning when running lr_target_prior_cor_inference()
#24
VivianQM
closed
1 year ago
6
All values in fraction_expressing_ligand_receptor column in prioritization_table_oi are 0
#23
catsargent
closed
1 year ago
6
No results returned when running get_top_n_lr_pairs
#22
catsargent
closed
1 year ago
2
Error in UseMethod("inner_join") when running make_lite_output
#21
catsargent
closed
1 year ago
1
Issue with parallelization of `get_ligand_activities_targets_DEgenes` on some systems
#20
browaeysrobin
opened
1 year ago
4
Bug `get_DE_info` when option `findMarkers = TRUE`
#19
browaeysrobin
closed
10 months ago
1
Error with cell type names containing spaces
#18
koelschnj
closed
1 year ago
1
Error: not enough samples when there are
#17
lo2811
closed
1 year ago
5
Error !is.null(pbs[["group_id"]]) is not TRUE
#16
carolinemorrell
closed
1 year ago
14
Issue with dplyr::standardise_join_by() with get_abundance_expression_info
#15
khain2650
closed
1 year ago
1
abundance_expression_info contains empty dfs
#14
avdl25
closed
1 year ago
1
Are logcounts required in sce object?
#13
catsargent
closed
1 year ago
5
Error in `auto_copy()`: Set `copy = TRUE` if `y` can be copied to the same source as `x` (may be slow).
#12
catsargent
closed
1 year ago
1
Error in `dplyr::inner_join()`: Problem with `ligand` and `target`.
#11
catsargent
closed
1 year ago
2
Error calling graph_plot$plot
#10
SergioRodLla
closed
10 months ago
8
How should I set the contrast table
#9
ziyangliu93
closed
1 year ago
5
NAs in "target" and "ligand_target_weighted" columns `ligand_activities_targets_DEgenes$ligand_activities` dataframe
#8
browaeysrobin
closed
1 year ago
1
Error when running get_DE_info()
#7
VivianQM
closed
1 year ago
30
Unable to install multinichenetr
#6
Sphiltje
closed
1 year ago
3
issue with filtering of genes before DE analysis
#5
browaeysrobin
closed
2 years ago
0
senders and receivers selection for input multinichenet wrapper function
#4
browaeysrobin
closed
2 years ago
0
Nichenet v2 networks and matrices compatibility with nichenetr pipeline
#3
ultimatex5
closed
2 years ago
1
get_abundance_expression_info changes category names that causes downstream error
#2
muratcemkose
closed
1 year ago
3
Vignettes not up-to-date
#1
browaeysrobin
closed
2 years ago
0
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