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This is the development version of DropletUtils; for the stable release version, see DropletUtils.

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: Development (3.20)

Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

Author: Aaron Lun [aut], Jonathan Griffiths [ctb, cre], Davis McCarthy [ctb], Dongze He [ctb], Rob Patro [ctb]

Maintainer: Jonathan Griffiths <jonathan.griffiths.94 at>

Citation (from within R, enter citation("DropletUtils")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Utilities for handling droplet-based single-cell RNA-seq data HTML R Script
Reference Manual PDF


biocViews Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.25.2
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends SingleCellExperiment
Imports utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, SparseArray(>= 1.5.18), DelayedArray(>= 0.31.9), DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle
System Requirements C++11, GNU make
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Suggests testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
Linking To Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Depends On Me OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me FLAMES, scCB2, scPipe, singleCellTK, Spaniel, SpatialFeatureExperiment
Suggests Me alabaster.spatial, demuxmix, mumosa, Nebulosa, SingleCellAlleleExperiment, SpatialExperiment, SPOTlight, tidySpatialExperiment, DropletTestFiles, MerfishData, muscData, spatialLIBD, scCustomize, SoupX
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package DropletUtils_1.25.2.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) DropletUtils_1.25.2.tgz
macOS Binary (arm64) DropletUtils_1.25.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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