scuttle

Legacy Utilities for Single-Cell RNA-Seq Analysis

Bioconductor version: 3.23 · Package version: 1.22.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scuttle")

Details

Maintainer	Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Author	Aaron Lun [aut, cre], Davis McCarthy [aut]
License	GPL-3
System Requirements	C++17
Downloads rank	12256
Source branch	RELEASE_3_23
biocViews	DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Documentation

Legacy utilities for single-cell RNA-seq analysis

Download

Source package

Dependencies

Depends: SingleCellExperiment

Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat

LinkingTo: Rcpp, beachmat, assorthead

Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran

Reverse dependencies

Depends On Me (3): omicsGMF, scater, scran

Imports Me (26): BASiCS, BASiCStan, batchelor, chevreulPlot, chevreulProcess, ClusterGVis, DESpace, DropletUtils, epiregulon, FLAMES, miaDash, mixhvg, mumosa, muscat, SanityR, scDblFinder, simPIC, singIST, singleCellTK, SpaceTrooper, SpatialArtifacts, spatialLIBD, splatter, SplineDV, spoon, velociraptor

Suggests Me (36): Banksy, bluster, CSOA, dreamlet, epiregulon.extra, escheR, futurize, ggsc, GSABenchmark, hammers, HCAData, iSEEde, iSEEfier, iSEEpathways, LISTO, mastR, mia, miloR, MouseThymusAgeing, raer, ReactomeGSA, SCArray, scConform, scCustomize, scDiagnostics, scDotPlot, schex, Seqtometry, SingleCellAlleleExperiment, sketchR, smoothclust, SpotSweeper, StatescopeR, SVP, tpSVG, TSCAN

Links To Me (2): DropletUtils, scran