scater
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see scater.
Single-cell analysis toolkit for gene expression data in R
Bioconductor version: 3.6
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.
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 "3.4") 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
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.6.3 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.4), Biobase, ggplot2, SingleCellExperiment, SummarizedExperiment |
| Imports | biomaRt, BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm, grid, limma, Matrix, matrixStats, methods, parallel, plyr, reshape2, rhdf5, rjson, S4Vectors, shiny, shinydashboard, stats, tximport, utils, viridis, Rcpp |
| System Requirements | C++11 |
| URL | http://bioconductor.org/packages/scater/ |
| Bug Reports | https://support.bioconductor.org/ |
See More
| Suggests | BiocStyle, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, testthat, magrittr |
| Linking To | Rhdf5lib, Rcpp, beachmat |
| Enhances | |
| Depends On Me | splatter |
| Imports Me | scran |
| Suggests Me | monocle, SC3, slalom |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scater_1.6.3.tar.gz |
| Windows Binary | scater_1.6.3.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | scater_1.6.3.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 | https://bioconductor.org/packages/scater/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |