DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils    

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: Release (3.11)

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, cre], Jonathan Griffiths [ctb], Davis McCarthy [ctb]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	1.8.0
In Bioconductor since	BioC 3.7 (R-3.5) (2.5 years)
License	GPL-3
Depends	SingleCellExperiment
Imports	S4Vectors, BiocParallel, Rcpp, Matrix, methods, utils, stats, edgeR, rhdf5, HDF5Array, R.utils, dqrng
LinkingTo	Rcpp, beachmat, Rhdf5lib, BH, dqrng
Suggests	testthat, beachmat, knitr, BiocStyle, rmarkdown
SystemRequirements	C++11, GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me	muscData, scater, splatter
Links To Me
Build Report

Package Archives

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

Source Package	DropletUtils_1.8.0.tar.gz
Windows Binary	DropletUtils_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	DropletUtils_1.8.0.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
Old Source Packages for BioC 3.11	Source Archive