scone
Single Cell Overview of Normalized Expression data
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scone")Details
| Maintainer | Davide Risso <risso.davide@gmail.com> |
| Author | Michael Cole [aut, cph], Davide Risso [aut, cre, cph], Matteo Borella [ctb], Chiara Romualdi [ctb] |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/YosefLab/scone/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/scone/ |
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.
Documentation
Download
Follow the 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 (arm64) | scone_1.36.0.tgz |
| macOS binary (x86_64) | scone_1.36.0.tgz |
Dependencies
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)
Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData