DropletUtils
This is the development version of DropletUtils; for the stable release version, see DropletUtils.
Utilities for Handling Single-Cell Droplet Data
Bioconductor version: Development (3.24)
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("DropletUtils")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.33.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL-3 |
| 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) |
| System Requirements | C++17, GNU make |
| URL |
See More
| Suggests | testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles |
| Linking To | Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows, scrapbook |
| Imports Me | DOtools, scCB2, scider, scPipe, singleCellTK, SpaceTrooper, Spaniel, SpatialExperimentIO, SpatialFeatureExperiment, stPipe, visiumStitched, OSTA |
| Suggests Me | alabaster.spatial, demuxmix, GEOquery, mumosa, Nebulosa, OSTA.data, SingleCellAlleleExperiment, SpatialExperiment, SPOTlight, SVP, tidySpatialExperiment, DropletTestFiles, MerfishData, muscData, spatialLIBD, nemoR, scCustomize, SoupX |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DropletUtils_1.33.0.tar.gz |
| Windows Binary (x86_64) | DropletUtils_1.33.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DropletUtils_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | DropletUtils_1.33.0.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/ |
| Package Downloads Report | Download Stats |