chrkuo

Bayespace reference scRNAseq data

3

Thank you for creating such a wonderful tool. Quick question - I read the BayesSapce paper and I am a bit confused - can this tool be used without a...

Giotto Object to STdeconvolve, and general questions about workflow, choosing K, cell type annotation, etc

12

Thank you so much for creating this tool for deconvolution without scRNAseq data. I am working with an extremely rare pediatric tumor where the samples are few and far between...

location of the deconvoluted spots

2

Hi, I am wondering after deconvolution is it possible to see which specific "spot" has what proportions of cell types and in return look at that spots gene enrichment and...

neighborhood analysis error

3

Hi, I am hitting an error code when I run neighborhood analysis: > FeatureOverlay(se_EWS4064_normalized, features = "nbs_2", ncols = 2, sampleids = 1:2, cols = c("red", "lightgray"), pt.size = 2)...

Hi seruat team, I have a analytic question: I have 2 scRNAseq samples from the same patient done at the same time (presumably no batch effect). since they're essentially from...

subset and re-integrate into the original object metadata and active.ident

8

Hi I am hitting multiple errors as I try to manuever subsetting and reannotating. I have an original object that I am trying to subcluster and reannotate that subcluster. After...

graph output spot size

1

Hi, thank you for the RCTD tool, I am wondering if there's anyway of adjusting the spot size on the graphs generated via these functions: plot_weights_doublet(cell_type_names, spatialRNA, resultsdir, results$weights_doublet, results$results_df)...