multipletR | The problem | The approach | Installation | The input: Cell Ranger's GEM classification file | How the data is generated | Where to find it | What it contains | Why this is the input multipletR needs | Column-name flexibility | Detecting multiplets | Reading the diagnostic plots | Adjusting the thresholds | Using the results with Seurat or SingleCellExperiment | Functions | How it works | Session info
Package: multipletR 0.99.0
Alexandra Gerveni
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.
Authors:
multipletR_0.99.0.tar.gz
multipletR_0.99.0.zip(r-4.7)multipletR_0.99.0.zip(r-4.6)multipletR_0.99.0.zip(r-4.5)
multipletR_0.99.0.tgz(r-4.6-any)multipletR_0.99.0.tgz(r-4.5-any)
multipletR_0.99.0.tar.gz(r-4.7-any)multipletR_0.99.0.tar.gz(r-4.6-any)
multipletR_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
multipletR/json (API)
| # Install 'multipletR' in R: |
| install.packages('multipletR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alex05a/multipletr/issues
singlecellrnaseqpreprocessingqualitycontroltranscriptomics
Last updated from:053f1b5922. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 199 | ||
| linux-devel-x86_64 | OK | 244 | ||
| source / vignettes | OK | 303 | ||
| linux-release-x86_64 | OK | 320 | ||
| macos-release-arm64 | OK | 178 | ||
| macos-oldrel-arm64 | OK | 187 | ||
| windows-devel | OK | 210 | ||
| windows-release | OK | 220 | ||
| windows-oldrel | OK | 319 | ||
| wasm-release | OK | 165 |
Exports:detect_multipletsremove_multiplets
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArraydiptestfarvergenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglatticelifecycleMatrixMatrixGenericsmatrixStatspatchworkR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Detect human-mouse multiplets in PDX single-cell data | detect_multiplets |
| Annotate (and optionally remove) multiplets in a Seurat or SingleCellExperiment object | remove_multiplets |
