scuttle
This is the development version of scuttle; for the stable release version, see scuttle.
Single-Cell RNA-Seq Analysis Utilities
Bioconductor version: Development (3.18)
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 "4.3") 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 | 1.11.2 |
In Bioconductor since | BioC 3.12 (R-4.0) (3 years) |
License | GPL-3 |
Depends | SingleCellExperiment |
Imports | methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat |
Linking To | Rcpp, beachmat |
Suggests | BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran |
System Requirements | C++11 |
Enhances | |
URL |
See More
Depends On Me | scater, scran |
Imports Me | BASiCS, BASiCStan, batchelor, DropletUtils, FLAMES, imcRtools, mia, mumosa, muscat, scDblFinder, singleCellTK, spatialHeatmap, spatialLIBD, splatter, velociraptor |
Suggests Me | bluster, DESpace, HCAData, mastR, miloR, MouseThymusAgeing, SCArray, SingleR, TSCAN |
Links To Me | DropletUtils, scran |
Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | scuttle_1.11.2.tar.gz |
Windows Binary | scuttle_1.11.2.zip |
macOS Binary (x86_64) | scuttle_1.11.2.tgz |
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 |