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Single Cell Overview of Normalized Expression data

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
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Suggests BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData
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Follow Installation instructions to use this package in your R session.

Source Package scone_1.28.0.tar.gz
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macOS Binary (x86_64) scone_1.28.0.tgz
macOS Binary (arm64) scone_1.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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