Package: multipletR
Type: Package
Title: Adaptive Detection of Human-Mouse Multiplets in PDX Single-Cell
        Data
Version: 0.99.9
Authors@R: c(
    person("Alexandra", "Gerveni",
           email = "alexandra.gerveni@hotmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0009-0004-5428-5889")),
    person("Amy", "Olex", role = "aut"),
    person("Mikhail", "Dozmorov", role = c("aut", "fnd"),
           comment = "P50AA022537"),
    person("Gamze", "Bulut", role = "aut"),
    person("J. Chuck", "Harrell", role = "fnd",
           comment = "U54CA283762"),
    person("Jose", "Trevino", role = "fnd",
           comment = "U54CA283762"))
Description: Detects human-mouse multiplets in patient-derived
        xenograft (PDX) single-cell RNA-seq data using an adaptive
        threshold method that does not assume a fixed species
        proportion. Takes a 10x CellRanger GEM classification file and
        returns the data with added multiplet classifications, with
        optional diagnostic plots and helpers to annotate a Seurat or
        SingleCellExperiment object with multiplet classifications or
        remove multiplets from it. The adaptive approach starts from a
        conservative central region of balanced droplets and expands
        its thresholds until the selected cells no longer resemble true
        multiplets, which handles the imbalanced species mixtures
        common in real PDX samples.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: diptest, ggplot2, methods, patchwork, scales,
        SingleCellExperiment, stats, utils
Suggests: BiocStyle, Seurat, SummarizedExperiment, knitr, rmarkdown,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: SingleCell, RNASeq, Preprocessing, QualityControl,
        Transcriptomics, Classification
URL: https://github.com/Alex05a/multipletR
BugReports: https://github.com/Alex05a/multipletR/issues
Config/testthat/edition: 3
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-22 01:42:01 UTC
RemoteUrl: https://github.com/bioc/multipletR
RemoteRef: HEAD
RemoteSha: a3af58a3c95a2917fc107393129e15e811668719
NeedsCompilation: no
Packaged: 2026-10-01 00:18:53 UTC; root
Author: Alexandra Gerveni [aut, cre] (ORCID:
    <https://orcid.org/0009-0004-5428-5889>),
  Amy Olex [aut],
  Mikhail Dozmorov [aut, fnd] (P50AA022537),
  Gamze Bulut [aut],
  J. Chuck Harrell [fnd] (U54CA283762),
  Jose Trevino [fnd] (U54CA283762)
Maintainer: Alexandra Gerveni <alexandra.gerveni@hotmail.com>