scone
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see scone.
Single Cell Overview of Normalized Expression data
Bioconductor version: 3.10
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]
Maintainer: Davide Risso <risso.davide at gmail.com>
citation("scone")):
Installation
To install this package, start R (version "3.6") 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")| scone Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.10.0 |
| 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 |
| 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, visNetwork, doParallel, BatchJobs |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scone_1.10.0.tar.gz |
| Windows Binary | scone_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | scone_1.10.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |