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 (3.20)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.25.2 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 |
| System Requirements | C++11, GNU make |
| URL |
See More
| Suggests | testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles |
| Linking To | Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle |
| Enhances | |
| Depends On Me | OSCA.intro, OSCA.workflows |
| Imports Me | FLAMES, scCB2, scPipe, singleCellTK, Spaniel, SpatialFeatureExperiment |
| Suggests Me | alabaster.spatial, demuxmix, mumosa, Nebulosa, SingleCellAlleleExperiment, SpatialExperiment, SPOTlight, tidySpatialExperiment, DropletTestFiles, MerfishData, muscData, spatialLIBD, 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_1.25.2.tar.gz |
| Windows Binary (x86_64) | DropletUtils_1.25.2.zip |
| macOS Binary (x86_64) | DropletUtils_1.25.2.tgz |
| macOS Binary (arm64) | DropletUtils_1.25.2.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 |