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DropletUtils (development version)

DropletUtils

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

Utilities for Handling Single-Cell Droplet Data

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DOI: 10.18129/B9.bioc.DropletUtils

Bioconductor version: Development (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")):

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Version 1.31.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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

System Requirements C++17, GNU make

URL

See More

Suggests testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles

Linking To Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle

Enhances

Depends On Me OSCA.intro, OSCA.multisample, OSCA.workflows

Imports Me DOtools, scCB2, scPipe, singleCellTK, SpaceTrooper, Spaniel, SpatialExperimentIO, SpatialFeatureExperiment, stPipe, visiumStitched

Suggests Me alabaster.spatial, demuxmix, GEOquery, mumosa, Nebulosa, OSTA.data, SingleCellAlleleExperiment, SpatialExperiment, SPOTlight, SVP, tidySpatialExperiment, DropletTestFiles, MerfishData, muscData, spatialLIBD, scCustomize, SoupX

Links To Me

Build Report Build Report

Package Archives

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

Source Package DropletUtils_1.31.0.tar.gz

Windows Binary (x86_64)

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

Bioc Package Browser https://code.bioconductor.org/browse/DropletUtils/

Package Short Url https://bioconductor.org/packages/DropletUtils/

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