Package: scone 1.36.0

Davide Risso

scone: Single Cell Overview of Normalized Expression data

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.

Authors:Michael Cole [aut, cph], Davide Risso [aut, cre, cph], Matteo Borella [ctb], Chiara Romualdi [ctb]

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manual.pdf |manual.html✨
card.svg |card.png
scone/json (API)
NEWS

# Install 'scone' in R:

install.packages('scone', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yoseflab/scone/issues

Datasets:

cellcycle_genes - Data: Positive and Negative Control Genes
cortical_markers - Data: Positive and Negative Control Genes
housekeeping - Data: Positive and Negative Control Genes
housekeeping_revised - Data: Positive and Negative Control Genes

On BioConductor:scone-1.37.0(bioc 3.24)scone-1.36.0(bioc 3.23)

immunooncology normalization preprocessing qualitycontrol geneexpression rnaseq software transcriptomics sequencing singlecell coverage

8.84 score 55 stars 106 scripts 556 downloads 5 mentions 38 exports 175 dependencies

Last updated from:37e98ec5b8 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	345
linux-devel-x86_64	NOTE	778
source / vignettes	OK	535
linux-release-x86_64	NOTE	729
macos-release-arm64	NOTE	505
macos-oldrel-arm64	NOTE	781
windows-devel	NOTE	1006
windows-release	NOTE	965
windows-oldrel	NOTE	894
wasm-release	OK	294

Exports:biplot_color biplot_interactive CLR_FN DESEQ_FN estimate_ziber factor_sample_filter fast_estimate_ziber FQ_FN FQT_FN get_batch get_bio get_design get_negconeval get_negconruv get_normalized get_params get_poscon get_qc get_score_ranks get_scores impute_expectation impute_null lm_adjust make_design metric_sample_filter PsiNorm PSINORM_FN scone scone_easybake SconeExperiment sconeReport score_matrix SCRAN_FN select_methods simple_FNR_params SUM_FN TMM_FN UQ_FN

Dependencies:abind AnnotationDbi aroma.light askpass base64enc bayesm BH Biobase BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob boot bslib cachem caTools cigarillo class cli cluster codetools compositions cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir DEoptimR digest diptest dir.expiry dplyr EDASeq edgeR evaluate farver fastmap filelock flexmix fontawesome formatR fpc fs futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gplots gtable gtools hexbin highr hms htmltools htmlwidgets httr httr2 hwriter interp IRanges isoband jpeg jquerylib jsonlite KEGGREST kernlab KernSmooth knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime mixtools modeltools nlme nnet openssl otel pillar pkgconfig plotly png prabclus prettyunits progress promises purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs rARPACK RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown robustbase Rsamtools RSpectra RSQLite rtracklayer RUVSeq S4Arrays S4Vectors S7 sass scales segmented Seqinfo ShortRead SingleCellExperiment snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tensorA tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xml2 XVector yaml

Introduction to SCONE

Michael Cole and Davide Risso

Rendered fromsconeTutorial.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-03-07
Started: 2016-11-15

PsiNorm: a scalable normalization for single-cellRNA-seq data

Matteo Borella, Chiara Romualdi, and Davide Risso

Rendered fromPsiNorm.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-07-07
Started: 2021-05-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function for biplotting with no point labels and with points color-coded according to a quantitative variable. For example: the rank of normalization performance.	biplot_color
Interactive biplot	biplot_interactive
Centered log-ratio (CLR) normalization wrapper function	CLR_FN
Data: Positive and Negative Control Genes	cellcycle_genes control_genes cortical_markers housekeeping housekeeping_revised
Relative log-expression (RLE; DESeq) scaling normalization wrapper function	DESEQ_FN
Parameter estimation of zero-inflated bernoulli model	estimate_ziber
Factor-based Sample Filtering: Function to filter single-cell RNA-Seq libraries.	factor_sample_filter
Fast parameter estimation of zero-inflated bernoulli model	fast_estimate_ziber
Full-quantile normalization wrapper function	FQT_FN FQ_FN
Get Factor of Biological Conditions and Batch	get_batch get_batch,SconeExperiment-method get_bio get_bio,SconeExperiment-method
Retrieve Design Matrix	get_design get_design,SconeExperiment,character-method get_design,SconeExperiment,numeric-method
Get Negative and Positive Controls	get_negconeval get_negconeval,SconeExperiment-method get_negconruv get_negconruv,SconeExperiment-method get_poscon get_poscon,SconeExperiment-method
Retrieve Normalized Matrix	get_normalized get_normalized,SconeExperiment,character-method get_normalized,SconeExperiment,numeric-method
Extract scone parameters	get_params get_params,SconeExperiment-method
Get Quality Control Matrix	get_qc get_qc,SconeExperiment-method
Extract scone scores	get_scores get_scores,SconeExperiment-method get_score_ranks get_score_ranks,SconeExperiment-method
Imputation of zero abundance based on general zero-inflated model	impute_expectation
Null or no-op imputation	impute_null
Linear Adjustment Normalization	lm_adjust
Make a Design Matrix	make_design
Metric-based Sample Filtering: Function to filter single-cell RNA-Seq libraries.	metric_sample_filter
PsiNorm: scaling normalization based on the Pareto distribution	PsiNorm PsiNorm,ANY-method PsiNorm,SingleCellExperiment-method PsiNorm,SummarizedExperiment-method
PsiNorm normalization wrapper	PSINORM_FN
Normalize Expression Data and Evaluate Normalization Performance	scone scone,SconeExperiment-method
Wrapper for Running Essential SCONE Modules	scone_easybake
Class SconeExperiment	SconeExperiment SconeExperiment,matrix-method SconeExperiment,SummarizedExperiment-method SconeExperiment-class
SCONE Report Browser: Browse Evaluation of Normalization Performance	sconeReport
SCONE Evaluation: Evaluate an Expression Matrix	score_matrix
Simple deconvolution normalization wrapper	SCRAN_FN
Get a subset of normalizations from a SconeExperiment object	select_methods select_methods,SconeExperiment,character-method select_methods,SconeExperiment,numeric-method
Fit Simple False-Negative Model	simple_FNR_params
Sum scaling normalization function	SUM_FN
Weighted trimmed mean of M-values (TMM) scaling normalization wrapper function	TMM_FN
Upper-quartile (UQ) scaling normalization wrapper function	UQ_FN