scater
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see scater.
Single-Cell Analysis Toolkit for Gene Expression Data in R
Bioconductor version: 3.8
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, cre], Kieran Campbell [aut], Aaron Lun [aut, ctb], Quin Wills [aut], Vladimir Kiselev [ctb]
Maintainer: Davis McCarthy <davis at ebi.ac.uk>
citation("scater")):
Installation
To install this package, start R (version "3.5") 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")| An introduction to the scater package | HTML | R Script |
| Data visualisation methods in scater | HTML | R Script |
| Quality control with scater | 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 | 1.10.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), SingleCellExperiment, ggplot2, BiocParallel |
| Imports | BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedMatrixStats, methods, plyr, reshape2, S4Vectors, stats, utils, viridis, Rcpp (>= 0.12.14), DelayedArray |
| System Requirements | C++11 |
| URL | http://bioconductor.org/packages/scater/ |
| Bug Reports | https://support.bioconductor.org/ |
See More
| Suggests | BiocStyle, biomaRt, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, umap, testthat, magrittr, pheatmap, irlba, tximport, tximportData, tximeta, Biobase, limma |
| Linking To | Rhdf5lib, Rcpp, beachmat |
| Enhances | |
| Depends On Me | netSmooth, simpleSingleCell |
| Imports Me | CATALYST, scran, splatter |
| Suggests Me | CellTrails, DuoClustering2018, iSEE, MAST, monocle, SC3, slalom, SummarizedBenchmark, TabulaMurisData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scater_1.10.1.tar.gz |
| Windows Binary | scater_1.10.1.zip |
| Mac OS X 10.11 (El Capitan) | scater_1.10.1.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 3.8 | Source Archive |