scater

DOI: 10.18129/B9.bioc.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 (from within R, enter citation("scater")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML R Script An introduction to the scater package
HTML R Script Data visualisation methods in scater
HTML R Script Quality control with scater
PDF   Reference Manual
Text   NEWS

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) (3 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
LinkingTo Rhdf5lib, Rcpp, beachmat
Suggests BiocStyle, biomaRt, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, umap, testthat, magrittr, pheatmap, irlba, tximport, tximportData, tximeta, Biobase, limma
SystemRequirements C++11
Enhances
URL http://bioconductor.org/packages/scater/
BugReports https://support.bioconductor.org/
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  

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
Package Short Url http://bioconductor.org/packages/scater/
Package Downloads Report Download Stats

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