DOI: 10.18129/B9.bioc.DropletUtils    

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

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: Development (3.15)

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 <infinite.monkeys.with.keyboards at gmail.com>, Jonathan Griffiths <infinite.monkeys.with.keyboards at gmail.com>, Davis McCarthy <infinite.monkeys.with.keyboards at gmail.com>, Dongze He <infinite.monkeys.with.keyboards at gmail.com>, Rob Patro <infinite.monkeys.with.keyboards at gmail.com>

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

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


To install this package, start R (version "4.2") and enter:

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

# The following initializes usage of Bioc devel


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


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biocViews Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.15.0
In Bioconductor since BioC 3.7 (R-3.5) (3.5 years)
License GPL-3
Depends SingleCellExperiment
Imports utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, SummarizedExperiment, BiocParallel, DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle
LinkingTo Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Suggests testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
SystemRequirements C++11, GNU make
Depends On Me
Imports Me scCB2, singleCellTK, Spaniel, SpatialExperiment
Suggests Me DropletTestFiles, mumosa, muscData, Nebulosa
Links To Me
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macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/DropletUtils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DropletUtils
Package Short Url https://bioconductor.org/packages/DropletUtils/
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