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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

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

Details

biocViews Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.23.0
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
See More
Suggests testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
Linking To Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Enhances
Depends On Me OSCA.intro, OSCA.multisample, OSCA.workflows
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 DropletUtils_1.23.0.tar.gz
Windows Binary DropletUtils_1.23.0.zip
macOS Binary (x86_64) DropletUtils_1.23.0.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/DropletUtils/
Package Short Url https://bioconductor.org/packages/DropletUtils/
Package Downloads Report Download Stats