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scone (development version)

scone

This is the development version of scone; for the stable release version, see scone.

Single Cell Overview of Normalized Expression data

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DOI: 10.18129/B9.bioc.scone

Bioconductor version: Development (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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")

Introduction to SCONE HTML R Script

PsiNorm normalization 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 1.35.0

In Bioconductor since BioC 3.5 (R-3.4) (8.5 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

See More

Suggests BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData

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Package Archives

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

Source Package scone_1.35.0.tar.gz

Windows Binary (x86_64) scone_1.35.0.zip

macOS Binary (x86_64) scone_1.35.0.tgz

macOS Binary (arm64) scone_1.35.0.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