scater
This is the development version of scater; for the stable release version, see scater.
Single-Cell Analysis Toolkit for Gene Expression Data in R
Bioconductor version: Development (3.20)
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
Author: Davis McCarthy [aut], Kieran Campbell [aut], Aaron Lun [aut, ctb], Quin Wills [aut], Vladimir Kiselev [ctb], Felix G.M. Ernst [ctb], Alan O'Callaghan [ctb, cre], Yun Peng [ctb], Leo Lahti [ctb] , Tuomas Borman [ctb]
Maintainer: Alan O'Callaghan <alan.ocallaghan at outlook.com>
citation("scater")
):
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("scater")
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("scater")
Overview of scater functionality | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
Version | 1.33.4 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
License | GPL-3 |
Depends | SingleCellExperiment, scuttle, ggplot2 |
Imports | stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr |
System Requirements | |
URL | http://bioconductor.org/packages/scater/ |
Bug Reports | https://support.bioconductor.org/ |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | scater_1.33.4.tar.gz |
Windows Binary | scater_1.33.4.zip (64-bit only) |
macOS Binary (x86_64) | scater_1.33.4.tgz |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/scater |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scater |
Bioc Package Browser | https://code.bioconductor.org/browse/scater/ |
Package Short Url | https://bioconductor.org/packages/scater/ |
Package Downloads Report | Download Stats |