In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

r h.i.r h.ii Doublet score estimation

if(results$doublet.method == "bcds"){
    cat("We estimate doublet score by using the binary classification based algorithm `bcds` in R package [scds](https://bioconductor.org/packages/release/bioc/html/scds.html).\n")
}else if(results$doublet.method == "cxds"){
    cat("We estimate doublet score by using the co-expression based algorithm `cxds` in R package [scds](https://bioconductor.org/packages/release/bioc/html/scds.html).\n")
}else if(results$doublet.method == "DoubletFinder"){
    cat("We estimate doublet score by using the algorithm in R package [DoubletFinder](https://github.com/chris-mcginnis-ucsf/DoubletFinder).\n")
}

The estimated doublet scores can be found in the column doublet.score of the table file cellAnnotation.txt.

Here is the scatter plot colored by the number of UMIs(left) and the estimated doublet scores(right).

plot_grid(results$nUMI.plot, results$doublet.plot, ncol = 2)

(Hi-res image: left, right)

h.ii <- h.ii + 1

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.