DropletUtils

DOI: 10.18129/B9.bioc.DropletUtils    

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: Release (3.7)

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 <alun at wehi.edu.au>

Citation (from within R, enter citation("DropletUtils")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("DropletUtils")

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, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.0.2
License GPL-3
Depends R (>= 3.5), BiocParallel, SingleCellExperiment
Imports S4Vectors, Matrix, methods, utils, stats, edgeR, Rcpp, rhdf5
LinkingTo Rcpp, beachmat, Rhdf5lib
Suggests testthat, beachmat, knitr, BiocStyle, rmarkdown, HDF5Array
SystemRequirements C++11
Enhances
URL
Depends On Me simpleSingleCell
Imports Me
Suggests Me scater
Build Report  

Package Archives

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

Source Package DropletUtils_1.0.2.tar.gz
Windows Binary DropletUtils_1.0.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DropletUtils_1.0.2.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
Old Source Packages for BioC 3.7 Source Archive

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