DropletUtils

This is the released version of DropletUtils; for the devel version, see DropletUtils.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: Release (3.23)

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 gmail.com>

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

Aaron Lun. DropletUtils: Utilities for Handling Single-Cell Droplet Data. doi:10.18129/B9.bioc.DropletUtils, R package version 1.32.1, https://bioconductor.org/packages/DropletUtils.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DropletUtils")

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

Documentation

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

browseVignettes("DropletUtils")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.32.1
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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 (>= 1.21.4)
System Requirements	C++17, GNU make
URL

Suggests	testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
Linking To	Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle
Enhances
Depends On Me
Imports Me	DOtools, scCB2, scider, scPipe, singleCellTK, SpaceTrooper, Spaniel, SpatialExperimentIO, SpatialFeatureExperiment, stPipe, visiumStitched
Suggests Me	alabaster.spatial, demuxmix, DropletTestFiles, GEOquery, MerfishData, mumosa, muscData, Nebulosa, nemoR, OSTA.data, scCustomize, SingleCellAlleleExperiment, smoppix, SoupX, SpatialExperiment, spatialLIBD, SPOTlight, SVP, tidySpatialExperiment
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DropletUtils_1.32.1.tar.gz
Windows Binary (x86_64)	DropletUtils_1.32.1.zip
macOS Binary (big-sur-x86_64)	DropletUtils_1.32.1.tgz
macOS Binary (sonoma-arm64)	DropletUtils_1.32.1.tgz
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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive