Comprehensive reporting of droplet QC metrics: identifying empty droplets using emptyDrops"

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

require(singleCellTK)
require(ggplot2)
require(umap)

sce<- params$object

    plotsEmptyDrops<- suppressWarnings(plotEmptyDropsResults(sce))
    i="EmptyDrops"
    cat(paste0('# ', i, ' {.tabset .tabset-fade} \n\n'))
    cat(paste0('## EmptyDrops, Total UMI counts vs Log-Probability \n\n'))
    plotsEmptyDrops$scatterEmptyDrops[[1]]
    cat(paste0('## Session info \n\n'))
    sce@metadata$runEmptyDrops

description_runEmptyDrops <- descriptionEmptyDrops()

{.unlisted .unnumbered .toc-ignore}

r description_runEmptyDrops

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.