This is the development version of scde; for the stable release version, see scde.
Single Cell Differential ExpressionBioconductor version: Development (3.22)
The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).
Author: Peter Kharchenko [aut, cre], Jean Fan [aut], Evan Biederstedt [aut]
Maintainer: Evan Biederstedt <evan.biederstedt at gmail.com>
Citation (from within R, entercitation("scde")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scde")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation Details biocViews Bayesian, DifferentialExpression, ImmunoOncology, RNASeq, Software, StatisticalMethod, Transcription Version 2.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License GPL-2 Depends R (>= 3.0.0), flexmix Imports Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel System Requirements URL http://pklab.med.harvard.edu/scde Bug Reports https://github.com/hms-dbmi/scde/issues See More Package ArchivesFollow Installation instructions to use this package in your R session.
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