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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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Spatial transcriptomic data compatibilty? #40

Open rajeha opened 1 year ago

rajeha commented 1 year ago

Hey @wguo-research, thank you for sharing this tool! Is it possible to apply this method for spatial 10X data? I saw it referenced in spatial transcriptomic papers. I started with runScStatistics, which runs for a bit then produces the following error:

....
[2023-01-25 20:25:27] -----: mito & ribo & diss distribution plot
[2023-01-25 20:25:29] -----: gene statistics
[2023-01-25 20:25:29] -----: gene proportion plot
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': error in evaluating the argument 'x' in selecting a method for function 't': invalid character indexing
In addition: Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In min(outliers) : no non-missing arguments to min; returning Inf
wguo-research commented 1 year ago

You can try our new package stCancer, which is specially designed for cancer spatial transcriptomics data analysis.