scone
Single Cell Overview of Normalized Expression data
Bioconductor version: Release (3.20)
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 "4.4") 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")| Introduction to SCONE | HTML | R Script |
| PsiNorm normalization | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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 |
| 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, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData |
| 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_1.30.0.tar.gz |
| Windows Binary (x86_64) | scone_1.30.0.zip (64-bit only) |
| macOS Binary (x86_64) | scone_1.30.0.tgz |
| macOS Binary (arm64) | scone_1.29.1.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 |