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Bioconductor - 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

Bioconductor version: Development (3.22)

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 "4.5") 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 1.29.4 In Bioconductor since BioC 3.7 (R-3.5) (7 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.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows Imports Me FLAMES, scCB2, scPipe, Spaniel, SpatialExperimentIO, SpatialFeatureExperiment, visiumStitched Suggests Me alabaster.spatial, demuxmix, 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.

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