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 (3.19)

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 gmail.com>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DropletUtils")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

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
URL

Suggests	testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
Linking To	Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Enhances
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
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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