DropletUtils

Utilities for Handling Single-Cell Droplet Data

Bioconductor version: 3.23 · Package version: 1.32.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DropletUtils")

Details

Maintainer	Jonathan Griffiths <jonathan.griffiths.94@gmail.com>
Author	Aaron Lun [aut], Jonathan Griffiths [ctb, cre], Davis McCarthy [ctb], Dongze He [ctb], Rob Patro [ctb]
License	GPL-3
System Requirements	C++17, GNU make
Downloads rank	3156
Source branch	RELEASE_3_23
biocViews	Coverage, DataImport, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Documentation

Utilities for handling droplet-based single-cell RNA-seq data

Download

Source package

Dependencies

Depends: SingleCellExperiment

Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9), DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle (>= 1.21.4)

LinkingTo: Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle

Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles

Reverse dependencies

Imports Me (11): DOtools, scCB2, scider, scPipe, singleCellTK, SpaceTrooper, Spaniel, SpatialExperimentIO, SpatialFeatureExperiment, stPipe, visiumStitched

Suggests Me (19): alabaster.spatial, demuxmix, DropletTestFiles, GEOquery, MerfishData, mumosa, muscData, Nebulosa, nemoR, OSTA.data, scCustomize, SingleCellAlleleExperiment, smoppix, SoupX, SpatialExperiment, spatialLIBD, SPOTlight, SVP, tidySpatialExperiment