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
git_url: https://git.bioconductor.org/packages/multipletR
git_branch: devel
git_last_commit: a3af58a
git_last_commit_date: 2026-09-21
Repository: Bioconductor 3.24
Date/Publication: 2026-09-29
NeedsCompilation: no
Packaged: 2026-09-29 22:06:31 UTC; biocbuild
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>
Built: R 4.6.1; ; 2026-09-30 06:09:40 UTC; unix
