Package: multipletR 0.99.9

multipletR: Adaptive Detection of Human-Mouse Multiplets in PDX Single-Cell Data

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.

Authors:Alexandra Gerveni [aut, cre], Amy Olex [aut], Mikhail Dozmorov [aut, fnd], Gamze Bulut [aut], J. Chuck Harrell [fnd], Jose Trevino [fnd]