doubletdetection: Doublet Detection
In scfurl/m3addon: This package adds to the popular "monocle3"

Description Usage Arguments Value References

See Gayoso, Adam, & Shor, Jonathan. (2018, July 17). DoubletDetection (Version v2.4). Zenodo. http://doi.org/10.5281/zenodo.2678042

doubletdetection(
  cds,
  python_home = system("which python", intern = TRUE),
  module_file = paste(system.file(package = "m3addon"), "doubletdetection.py", sep =
    "/"),
  boost_rate = 0.25,
  n_components = 30,
  n_top_var_genes = 10000,
  use_phenograph = TRUE,
  n_iters = 25,
  verbose = TRUE,
  standard_scaling = FALSE,
  p_thresh = 1e-07,
  voter_thresh = 0.9
)

`cds`	the CellDataSet upon which to perform Scrublet
`python_home`	The python home directory where doubletdetection is installed
`boost_rate`	(float, optional): Proportion of cell population size to produce as synthetic doublets.
`n_components`	(int, optional): Number of principal components used for clustering.
`n_top_var_genes`	(int, optional): Number of highest variance genes to use; other genes discarded. Will use all genes when zero. replace (bool, optional): If False, a cell will be selected as a synthetic doublet's parent no more than once.
`use_phenograph`	(bool, optional): Set to False to disable PhenoGraph clustering in exchange for louvain clustering implemented in scanpy. Defaults to True.
`n_iters`	(int, optional): Number of fit operations from which to collect p-values. Defualt value is 25.
`verbose`	(bool, optional): Set to False to silence all normal operation informational messages. Defaults to True.
`standard_scaling`	(bool, optional): Set to True to enable standard scaling of normalized count matrix prior to PCA. Recommended when not using Phenograph. Defaults to False.
`p_thresh`	(float, optional): hypergeometric test p-value threshold that determines per iteration doublet calls
`voter_thresh`	(float, optional): fraction of iterations a cell must be called a doublet