scone
This is thereleased version of scone; for the devel version, seescone.
Single Cell Overview of Normalized Expression data
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("scone")For older versions of R, please refer to the appropriateBioconductor 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 | 1.34.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | scone_1.34.0.tar.gz |
| Windows Binary (x86_64) | scone_1.34.0.zip |
| macOS Binary (x86_64) | scone_1.34.0.tgz |
| macOS Binary (arm64) | scone_1.34.0.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 |