doubletFinder_v3: doubletFinder
In scfurl/m3addon: This package adds to the popular "monocle3"

Core doublet prediction function of the DoubletFinder package. Generates artifical doublets from an existing, pre-processed cdsrat object. Real and artificial data are then merged and pre-processed using parameters utilized for the existing cdsrat object. PC distance matrix is then computed and used the measure the proportion of artificial nearest neighbors (pANN) for every real cell. pANN is then thresholded according to the number of expected doublets to generate final doublet predictions.

1	cds <- doubletFinder(cds, PCs, pN = 0.25, pK, nExp, reuse.pANN = FALSE)

`cds`	Input cell_data_set object.
`PCs`	Number of statistically-significant principal components (e.g., as estimated from PC elbow plot)
`pN`	The number of generated artificial doublets, expressed as a proportion of the merged real-artificial data. Default is set to 0.25, based on observation that DoubletFinder performance is largely pN-invariant (see McGinnis, Murrow and Gartner 2019, Cell Systems).
`pK`	The PC neighborhood size used to compute pANN, expressed as a proportion of the merged real-artificial data. No default is set, as pK should be adjusted for each scRNA-seq dataset. Optimal pK values can be determined using mean-variance-normalized bimodality coefficient.
`nExp`	The total number of doublet predictions produced. This value can best be estimated from cell loading densities into the 10X/Drop-Seq device, and adjusted according to the estimated proportion of homotypic doublets.
`genes`	if "all", use all genes; if "recalc", recalculate ordering genes using `calculate_gene_dispersion` and `select_genes`, passing arguments to each of these functions using ....; if "same" use ordering genes specified in cds; or a vector of ordering genes to be used.
`...`	arguments passed to 1) `calculate_gene_dispersion` and 2) `select_genes`: note that default for top_n passsed to `select_genes` in this context is 2000 features. See specific function documentation for further information on acceptable arguments to be passed these functions.
`reuse.pANN`	Metadata column name for previously-generated pANN results. Argument should be set to FALSE (default) for initial DoubletFinder runs. Enables fast adjusting of doublet predictions for different nExp.