Package: DropletUtils 1.33.0

Jonathan Griffiths

DropletUtils: Utilities for Handling Single-Cell Droplet Data

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.

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

DropletUtils_1.33.0.tar.gz
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DropletUtils_1.33.0.tgz(r-4.6-x86_64)DropletUtils_1.33.0.tgz(r-4.6-arm64)DropletUtils_1.33.0.tgz(r-4.5-x86_64)DropletUtils_1.33.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
card.svg |card.png
DropletUtils/json (API)
NEWS

# Install 'DropletUtils' in R:
install.packages('DropletUtils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • c++– GNU Standard C++ Library v3

On BioConductor:DropletUtils-1.33.0(bioc 3.24)DropletUtils-1.32.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysinglecellsequencingrnaseqgeneexpressiontranscriptomicsdataimportcoveragecurlopensslcpp

10.45 score 13 packages 3.5k scripts 4.6k downloads 14 mentions 30 exports 50 dependencies

Last updated from:ebff365ae1. Checks:1 NOTE, 3 ERROR, 1 OK, 8 WARNING, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE232
linux-devel-arm64ERROR404
linux-devel-x86_64ERROR479
source / vignettesOK359
linux-release-arm64WARNING428
linux-release-x86_64WARNING476
macos-release-arm64WARNING367
macos-release-x86_64WARNING660
macos-oldrel-arm64WARNING237
macos-oldrel-x86_64WARNING589
windows-develERROR1457
windows-releaseWARNING1427
windows-oldrelWARNING1368
wasm-releaseFAIL189

Exports:ambientContribMaximumambientContribNegativeambientContribSparseambientProfileBimodalambientProfileEmptybarcodeRankschimericDropscleanTagCountscontrolAmbiencedefaultDropsdownsampleBatchesdownsampleMatrixdownsampleReadsemptyDropsemptyDropsCellRangerencodeSequencesestimateAmbienceget10xMolInfoStatshashedDropsinferAmbiencemakeCountMatrixmaximumAmbienceread10xCountsread10xMolInforemoveAmbienceremoveChimericDropsremoveSwappedDropsswappedDropstestEmptyDropswrite10xCounts

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsbiocmakeBiocParallelcodetoolscpp11DelayedArrayDelayedMatrixStatsdir.expirydqrngedgeRfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesh5mreadHDF5ArrayIRangeslambda.rlatticelimmalocfitMatrixMatrixGenericsmatrixStatsR.methodsS3R.ooR.utilsRcpprhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentXVector

Utilities for handling droplet-based single-cell RNA-seq data

Aaron Lun

Rendered fromDropletUtils.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2020-07-15
Started: 2017-12-21

Readme and manuals

Help Manual

Help pageTopics
Ambient contribution by maximum scalingambientContribMaximum ambientContribMaximum,ANY-method ambientContribMaximum,SummarizedExperiment-method maximumAmbience
Ambient contribution from negative controlsambientContribNegative ambientContribNegative,ANY-method ambientContribNegative,SummarizedExperiment-method controlAmbience
Ambient contribution by assuming sparsityambientContribSparse ambientContribSparse,ANY-method ambientContribSparse,SummarizedExperiment-method
Ambient profile from bimodalityambientProfileBimodal ambientProfileBimodal,ANY-method ambientProfileBimodal,SummarizedExperiment-method inferAmbience
Estimate the ambient profile from empty dropletsambientProfileEmpty ambientProfileEmpty,ANY-method ambientProfileEmpty,SummarizedExperiment-method estimateAmbience
Calculate barcode ranksbarcodeRanks barcodeRanks,ANY-method barcodeRanks,SummarizedExperiment-method
Remove chimeric moleculeschimericDrops removeChimericDrops
Clean a tag-based datasetcleanTagCounts cleanTagCounts,ANY-method cleanTagCounts,SummarizedExperiment-method
Call cells from their total number of UMIsdefaultDrops defaultDrops,ANY-method defaultDrops,SummarizedExperiment-method
Downsample reads in a 10X Genomics datasetdownsampleReads
Identify empty dropletsemptyDrops emptyDrops,ANY-method emptyDrops,SummarizedExperiment-method testEmptyDrops
CellRanger's emptyDrops variantemptyDropsCellRanger emptyDropsCellRanger,ANY-method emptyDropsCellRanger,SummarizedExperiment-method
Encode nucleotide sequencesencodeSequences
Get 10x cell statisticsget10xMolInfoStats
Demultiplex cell hashing datahashedDrops hashedDrops,ANY-method hashedDrops,SummarizedExperiment-method
Make a count matrixmakeCountMatrix
Load data from a 10X Genomics experimentread10xCounts
Read the 10X molecule information fileread10xMolInfo
Remove the ambient profileremoveAmbience removeAmbience,ANY-method removeAmbience,SummarizedExperiment-method
Clean barcode-swapped droplet dataremoveSwappedDrops swappedDrops
Write count data in the 10x formatwrite10xCounts