nichenetr

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Error at make_ligand_activity_target_exprs_plot()

2

Hi, thanks for the great package! I was trying the "differential_nichenet_pEMT.md" vignette using my own data , and it worked perfectly for most condition comparisons, until I stumbled into this...

Daliya-K

Conda package

8

Hi, would it be possible that you add nichenet to Bioconda? Thank you very much

Zethson

In `make_ligand_activity_target_exprs_plot`, the outer left plot is ordered based on the niche name, but the activity plots are ordered based on the receiver name

browaeysrobin

Seurat Wrapper + Circos visualization

1

I am trying to plot the Circo plot in this vingette, when I run: circos.par(gap.degree = gaps) chordDiagram(links_circle, directional = 1,order=order,link.sort = TRUE, link.decreasing = FALSE, grid.col = grid_col,transparency =...

chrismahony

nichenet through seurat-cell type specific ligand/receptor scores

4

Hello, first - very nice to finally see ligand receptor interaction connecting to gene expression :) I am using nichenet through seurat and I was wondering whether it's possible to...

annamath

Making a ligand-receptor-target circos plot

2

Thanks for this great package! I would like to make a ligand-receptor-target circos plot as described in the "circos" vignette and as seen in "B":  I...

abberclark

Hello Robin, I use the nichenet to understand if there is cross tissue communication for two physically closely linked tissues. My hypothesis is since they are so close, they may...

adesalegn

LIANA results as LR db input

2

I note LIANA releases a vignette that integrates LIANA and NicheNet to explore the data. I wonder do you have any plan to combine the LIANA approach with your method....

joe-jhou2

Differential nichenet Ligand-targets

1

Thank you for the wonderful package! From what I understand, the workflow of ranking putative ligands is to rank ligands based on how predictive they are for downstream genes. However...

ejc043

Differential expression SCT

12

Hello, I am performing NicheNet with SCTransformed-integrated data. I run PrepSCTFindMarkers() function before runing NicheNet for Seuratm but I keep getting error: > Error in if (any(unlist(model_median_umis) != min_median_umi)) {...

DzenisKoca