DOI: 10.18129/B9.bioc.DropletUtils  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DropletUtils.

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: 3.17

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>

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


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HTML R Script Utilities for handling droplet-based single-cell RNA-seq data
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biocViews Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 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
Depends On Me OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me FLAMES, scCB2, scPipe, singleCellTK, Spaniel, SpatialExperiment
Suggests Me demuxmix, DropletTestFiles, mumosa, muscData, Nebulosa, SpatialFeatureExperiment
Links To Me
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Source Package DropletUtils_1.20.0.tar.gz
Windows Binary DropletUtils_1.20.0.zip
macOS Binary (x86_64) DropletUtils_1.20.0.tgz
macOS Binary (arm64) DropletUtils_1.20.0.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/
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