CellChat

CellChat copied to clipboard

Hi @sqjin I'm wondering if it's possible to use CellChat with a list of LR pairs that does not contain complexes and cofactors (it's from another organism too). I tried...

earmingol

Bubble Plot - make size of bubble proportional to comm. probability

1

Hi Suoqin, I am wondering if it is possible to change the parameters of the netVisual_bubble function such that the SIZE of the bubbles (instead of the colours) on the...

EvelynZav

rankSimilarity Error: attempt to set 'rownames' on an object with no dimensions

1

Hello, I was attempting to run plots on merged cellchat dataset, the other functions run just fine except rankSimilarity, where an error message says: ``` rankSimilarity(cellchat, type = "functional") Error...

h1hui

netVisual_embeddingPairwise: error due to handling of 'pathway.remove'

4

Hi, Thanks for the great package! It seems like there's an issue in netVisual_embeddingPairwise related to removing pathways. Pathways to be removed are identified in the similarity matrix, where each...

ktessema

Error in netVisual_embeddingPairwise() - arguments imply differing number of rows

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Hello, and thank you for an excellent package - I've gotten a lot of good use out of it so far. I have a merged CellChat object built from four...

cgoneill

High expression level of receptor in one cell type but not showing up in results

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Hi, Thank you for this great package, I am really enjoying using it. I have a question: In my dataset (labelled prior), when focusing on one signaling pathway of interest,...

EvelynZav

"identifyOverExpressedGenes()" Same data but different results

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I got result A using a dataset of 20 cell lines. I extracted two cell lines from the same data set and calculated again, and got result B. A and...

wahahaaaa123

subsetCellChat() change the cellchat@netP$centr

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Hi, Thank you for the package! I have multiple group data and would like to identify major signaling changes. Due to the minor difference in cell type, I used subsetCellChat()...

RongDing-NMU

Doing stats across two datasets in merged CellChat

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Hello! Thank you so much for developing this incredibly useful tool! I merged two datasets with the same cell types to compare signaling from cell type 1 (het) to cell...

bayankizil

p-value digits for CellChat analysis

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Hi Authors, I'm a postdoc from UCSF and we uses your tool a lot. It helps greatly in our daily research. We are currently making figures for our next publication....

toushirou1220