DOI: 10.18129/B9.bioc.scone  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scone.

Single Cell Overview of Normalized Expression data

Bioconductor version: 3.16

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")):


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


biocViews Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.22.0
In Bioconductor since BioC 3.5 (R-3.4) (6 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
Suggests BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs, splatter, scater, kableExtra, mclust, TENxPBMCData
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