DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils    

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 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
LinkingTo	Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Suggests	testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles
SystemRequirements	C++11, GNU make
Enhances
URL
Depends On Me	OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me	scCB2, singleCellTK, Spaniel, SpatialExperiment
Suggests Me	DropletTestFiles, mumosa, muscData, Nebulosa
Links To Me
Build Report

Package Archives

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

Source Package	DropletUtils_1.16.0.tar.gz
Windows Binary	DropletUtils_1.16.0.zip
macOS Binary (x86_64)	DropletUtils_1.16.0.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