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Traditionally, supervised (manual) analysis involves drawing gates, drilling down with subsequent gates filtering for a desired cell population of interest. Combined with expert knowledge and few markers, it allows handling of batch effects. Unsupervised approaches have become more frequent employed with increased markers employed by both Spectral Flow Cytometry (SFC) and mass cytometry. Their limitation has been in addressing what is a cluster and how many of them should be present for a given panel.
Coereba is a collection of tools that attempt to allow the researcher to better understand their panels and datasets, employing a semi-supervised approach between the two approaches.
We are in the process of getting Coereba ready to submit to Bioconductor. Until then, please download the package from github.
if(!require("remotes")) install.packages("remotes")
remotes::install_github("https://github.com/DavidRach/Coereba")
library(Coereba)
# install.packages("BiocManager")
# BiocManager::install("Coereba")Please check out our how-to vignettes to get started
While we have caught a lot of bugs, there's still unknown ones that we haven't encountered. If you find a suspected bug, please report it here here