NICHES
NICHES copied to clipboard
msraredon
Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
Hi, Thank you for writing such a wonderful & useful tool! I am currently using this for my MERFISH data; and I noticed that with even one sample of 30,000...
I am trying to run NICHES analysis on a splitted, un-imputed data set. The data set has 6 samples (annotated by 'Condition'), and 13 cell types (annotated by 'Global_CellType_V2'). Some...
I have encountered an interesting bug, I think related to how we are calculating edgelists in spatial data. If I RunNICHES on imputed spatial data of reasonable size, I get...
Hi, Thanks for this great tool. NICHES has worked well for me in the past. However, now I am running into "Error: No cell overlap between new meta data and...
Hi, I got an error when running RunNiches() stating that Compute edgelist based on mutual nearest neighbors. Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double)...
Hi, I am running NICHES on a seurat object version ‘5.0.2’ and have been getting the below error. Any suggestions? Error in validObject(object = object) : invalid class “Assay5” object:...
Hi,I am currently working on a spatial transcriptomics analysis using NICHES packages in R. I encountered an error while running `RunNICHES()` that states: Error in UseMethod("mutate"): "mutate" has no applicable...
Hi, thanks for your great work. Considering the recent bugs in Seurat v5 as well as its complicated structure to load spatial data, do you have any plans to develop...
