scuttle
This is the released version of scuttle; for the devel version, see scuttle.
Legacy Utilities for Single-Cell RNA-Seq Analysis
Bioconductor version: Release (3.23)
Provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.
Author: Aaron Lun [aut, cre], Davis McCarthy [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("scuttle")):
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")
BiocManager::install("scuttle")
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("scuttle")| Single-cell utilities | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | SingleCellExperiment |
| Imports | methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat |
| System Requirements | C++17 |
| URL |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scuttle_1.22.0.tar.gz |
| Windows Binary (x86_64) | scuttle_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | scuttle_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | scuttle_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scuttle |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scuttle |
| Bioc Package Browser | https://code.bioconductor.org/browse/scuttle/ |
| Package Short Url | https://bioconductor.org/packages/scuttle/ |
| Package Downloads Report | Download Stats |