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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 (3.19)

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.


Reference Manual PDF


biocViews Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.23.1
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, DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle
System Requirements C++11, GNU make
See More
Suggests testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
Linking To Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Depends On Me
Imports Me FLAMES, scCB2, scPipe, singleCellTK, Spaniel, SpatialFeatureExperiment
Suggests Me alabaster.spatial, demuxmix, DropletTestFiles, MerfishData, mumosa, muscData, Nebulosa, SpatialExperiment, spatialLIBD, SPOTlight, tidySpatialExperiment
Links To Me
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