scone

DOI: 10.18129/B9.bioc.scone    

Single Cell Overview of Normalized Expression data

Bioconductor version: Release (3.8)

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

Author: Michael Cole [aut, cre, cph], Davide Risso [aut, cph]

Maintainer: Michael Cole <mbeloc at gmail.com>

Citation (from within R, enter citation("scone")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("scone", version = "3.8")

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("scone")

 

HTML R Script scone Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 years)
License Artistic-2.0
Depends R (>= 3.4), methods, SummarizedExperiment
Imports graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK
LinkingTo
Suggests BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork
SystemRequirements
Enhances
URL
BugReports https://github.com/YosefLab/scone/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scone_1.6.0.tar.gz
Windows Binary scone_1.6.0.zip
Mac OS X 10.11 (El Capitan) scone_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scone
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scone
Package Short Url http://bioconductor.org/packages/scone/
Package Downloads Report Download Stats

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