To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scater")
In most cases, you don't need to download the package archive at all.
scater
|
|
|
|
|
DOI: 10.18129/B9.bioc.scater
Single-cell analysis toolkit for gene expression data in R
Bioconductor version: Release (3.5)
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
Maintainer: Davis McCarthy <davis at ebi.ac.uk>
Citation (from within R,
enter citation("scater")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scater")
Documentation
| HTML | R Script | An introduction to the scater package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3), Biobase, ggplot2, methods |
| Imports | biomaRt, BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm, grid, limma, Matrix, matrixStats, parallel, plyr, reshape2, rhdf5, rjson, shiny, shinydashboard, stats, tximport, utils, viridis |
| LinkingTo | |
| Suggests | BiocStyle, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, testthat, magrittr |
| SystemRequirements | |
| Enhances | |
| URL | http://bioconductor.org/packages/scater/ |
| BugReports | https://support.bioconductor.org/ |
| Depends On Me | scran, splatter |
| Imports Me | Glimma, SC3 |
| Suggests Me | switchde |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scater_1.4.0.tar.gz |
| Windows Binary | scater_1.4.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | scater_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scater |
| Package Short Url | http://bioconductor.org/packages/scater/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
