scone

This is the released version of scone; for the devel version, see scone.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

Single Cell Overview of Normalized Expression data

Bioconductor version: Release (3.23)

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>

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

Michael Cole, Davide Risso. scone: Single Cell Overview of Normalized Expression data. doi:10.18129/B9.bioc.scone, R package version 1.36.0, https://bioconductor.org/packages/scone.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.36.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 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, DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6)
System Requirements
URL
Bug Reports	https://github.com/YosefLab/scone/issues

Suggests	BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	scone_1.36.0.tar.gz
Windows Binary (x86_64)	scone_1.36.0.zip
macOS Binary (big-sur-x86_64)	scone_1.36.0.tgz
macOS Binary (sonoma-arm64)	scone_1.36.0.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	https://bioconductor.org/packages/scone/
Package Downloads Report	Download Stats