scuttle
This is the development version of scuttle; for the stable release version, see scuttle.
Single-Cell RNA-Seq Analysis Utilities
Bioconductor version: Development (3.21)
Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.
Author: Aaron Lun [aut, cre], Davis McCarthy [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("scuttle")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| 1. Quality control | HTML | R Script |
| 2. Normalization | HTML | R Script |
| 3. Other functions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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++11 |
| URL |
See More
| Suggests | BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran |
| Linking To | Rcpp, beachmat |
| Enhances | |
| Depends On Me | scater, scran, OSCA.intro, OSCA.workflows, SingleRBook |
| Imports Me | BASiCS, BASiCStan, batchelor, DropletUtils, epiregulon, FLAMES, imcRtools, mia, mumosa, muscat, scDblFinder, simPIC, singleCellTK, splatter, SplineDV, spoon, velociraptor, spatialLIBD, mixhvg, SpatialDDLS |
| Suggests Me | Banksy, bluster, DESpace, dreamlet, epiregulon.extra, escheR, ggsc, iSEEde, iSEEfier, iSEEpathways, mastR, miloR, raer, ReactomeGSA, SCArray, scDiagnostics, scDotPlot, schex, SingleCellAlleleExperiment, SingleR, sketchR, smoothclust, spatialHeatmap, SpotSweeper, tpSVG, TSCAN, HCAData, MouseThymusAgeing, scCustomize |
| Links To Me | DropletUtils, scran |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scuttle_1.17.0.tar.gz |
| Windows Binary (x86_64) | scuttle_1.17.0.zip |
| macOS Binary (x86_64) | scuttle_1.17.0.tgz |
| macOS Binary (arm64) | scuttle_1.17.0.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 |