multipletR
This is the development version of multipletR; to use it, please install the devel version of Bioconductor.
Adaptive Detection of Human-Mouse Multiplets in PDX Single-Cell Data
Bioconductor version: Development (3.24)
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.
Author: Alexandra Gerveni [aut, cre]
, 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 at hotmail.com>
citation("multipletR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("multipletR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("multipletR")| Detecting human-mouse multiplets in PDX single-cell data with multipletR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Preprocessing, QualityControl, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | diptest, ggplot2, methods, patchwork, scales, SingleCellExperiment, stats, utils |
| System Requirements | |
| URL | https://github.com/Alex05a/multipletR |
| Bug Reports | https://github.com/Alex05a/multipletR/issues |
See More
| Suggests | BiocStyle, Seurat, SummarizedExperiment, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | multipletR_0.99.9.tar.gz |
| Windows Binary (x86_64) | multipletR_0.99.9.zip |
| macOS Binary (big-sur-x86_64) | multipletR_0.99.9.tgz |
| macOS Binary (sonoma-arm64) | multipletR_0.99.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/multipletR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/multipletR |
| Bioc Package Browser | https://code.bioconductor.org/browse/multipletR/ |
| Package Short Url | https://bioconductor.org/packages/multipletR/ |
| Package Downloads Report | Download Stats |