DropletUtils
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DropletUtils.
Utilities for Handling Single-Cell Droplet Data
Bioconductor version: 3.9
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>
citation("DropletUtils")):
Installation
To install this package, start R (version "3.6") 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")| Utilities for handling droplet-based single-cell RNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.4.3 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | GPL-3 |
| Depends | SingleCellExperiment |
| Imports | S4Vectors, BiocParallel, Rcpp, Matrix, methods, utils, stats, edgeR, rhdf5, HDF5Array, R.utils, dqrng |
| System Requirements | C++11 |
| URL |
See More
| Suggests | testthat, beachmat, knitr, BiocStyle, rmarkdown |
| Linking To | Rcpp, beachmat, Rhdf5lib, BH, dqrng |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | simpleSingleCell |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DropletUtils_1.4.3.tar.gz |
| Windows Binary | DropletUtils_1.4.3.zip |
| Mac OS X 10.11 (El Capitan) | DropletUtils_1.4.3.tgz |
| 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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |