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scuttle (development version)

scuttle

This is the development version of scuttle; for the stable release version, see scuttle.

Single-Cell RNA-Seq Analysis Utilities

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DOI: 10.18129/B9.bioc.scuttle

Bioconductor version: Development (3.23)

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 (from within R, enter citation("scuttle")):

Installation

To install this package, start R (version "4.6") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Version 1.21.0

In Bioconductor since BioC 3.12 (R-4.0) (5 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 omicsGMF, scater, scran, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook

Imports Me BASiCS, BASiCStan, batchelor, chevreulPlot, chevreulProcess, ClusterGVis, DESpace, DropletUtils, epiregulon, FLAMES, imcRtools, mia, miaDash, mumosa, muscat, SanityR, scDblFinder, simPIC, singleCellTK, SpaceTrooper, splatter, SplineDV, spoon, velociraptor, spatialLIBD, mixhvg, SpatialDDLS

Suggests Me Banksy, bluster, CSOA, dreamlet, epiregulon.extra, escheR, ggsc, GSVA, iSEEde, iSEEfier, iSEEpathways, mastR, miloR, raer, ReactomeGSA, SCArray, scDiagnostics, scDotPlot, schex, SingleCellAlleleExperiment, SingleR, sketchR, smoothclust, SpotSweeper, SVP, 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_1.21.0.tar.gz

Windows Binary (x86_64) scuttle_1.21.0.zip (64-bit only)

macOS Binary (x86_64)

macOS Binary (arm64)

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