scater
This is the released version of scater; for the devel version, see scater.
Single-Cell Analysis Toolkit for Gene Expression Data in R
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.40.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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 |
| 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_1.40.2.tar.gz |
| Windows Binary (x86_64) | scater_1.40.2.zip |
| macOS Binary (big-sur-x86_64) | scater_1.40.2.tgz |
| macOS Binary (sonoma-arm64) | scater_1.40.2.tgz |
| 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 |
| Old Source Packages for BioC 3.23 | Source Archive |