scone

DOI: 10.18129/B9.bioc.scone  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scone.

Single Cell Overview of Normalized Expression data

Bioconductor version: 3.17

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, cph], Davide Risso [aut, cre, cph], Matteo Borella [ctb], Chiara Romualdi [ctb]

Maintainer: Davide Risso <risso.davide at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scone")

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	Introduction to SCONE
HTML	R Script	PsiNorm normalization
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.24.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 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, MatrixGenerics, SingleCellExperiment
LinkingTo
Suggests	BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData
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_1.24.0.tar.gz
Windows Binary	scone_1.24.0.zip (64-bit only)
macOS Binary (x86_64)	scone_1.24.0.tgz
macOS Binary (arm64)	scone_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scone
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scone
Bioc Package Browser	https://code.bioconductor.org/browse/scone/
Package Short Url	https://bioconductor.org/packages/scone/
Package Downloads Report	Download Stats