scuttle
This is the development version of scuttle; for the stable release version, see scuttle.
Single-Cell RNA-Seq Analysis Utilities
Bioconductor version: Development (3.20)
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 "4.4") 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 | 1.15.4 |
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.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows |
Imports Me | BASiCS, BASiCStan, batchelor, DropletUtils, epiregulon, FLAMES, imcRtools, mia, mumosa, muscat, scDblFinder, simPIC, singleCellTK, splatter, spoon, velociraptor, spatialLIBD, digitalDLSorteR, mixhvg, SpatialDDLS |
Suggests Me | Banksy, bluster, DESpace, dreamlet, epiregulon.extra, escheR, ggsc, iSEEde, iSEEfier, iSEEpathways, mastR, miloR, raer, SCArray, 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_1.15.4.tar.gz |
Windows Binary | scuttle_1.15.4.zip |
macOS Binary (x86_64) | scuttle_1.15.0.tgz |
macOS Binary (arm64) | scuttle_1.15.1.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 |