DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DropletUtils.

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: 3.8

Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, 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 "3.5") 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	1.2.2
In Bioconductor since	BioC 3.7 (R-3.5) (1 year)
License	GPL-3
Depends	R (>= 3.5), BiocParallel, SingleCellExperiment
Imports	S4Vectors, Matrix, methods, utils, stats, edgeR, Rcpp, rhdf5, HDF5Array
LinkingTo	Rcpp, beachmat, Rhdf5lib
Suggests	testthat, beachmat, knitr, BiocStyle, rmarkdown
SystemRequirements	C++11
Enhances
URL
Depends On Me	simpleSingleCell
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DropletUtils_1.2.2.tar.gz
Windows Binary	DropletUtils_1.2.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	DropletUtils_1.2.2.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	http://bioconductor.org/packages/DropletUtils/
Package Downloads Report	Download Stats