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This is the development version of scde; for the stable release version, see scde.

Single Cell Differential Expression

Bioconductor version: Development (3.19)

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, enter citation("scde")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews Bayesian, DifferentialExpression, ImmunoOncology, RNASeq, Software, StatisticalMethod, Transcription
Version 2.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
Suggests knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown
Linking To Rcpp, RcppArmadillo
Depends On Me
Imports Me
Suggests Me pagoda2
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scde_2.31.0.tar.gz
Windows Binary scde_2.31.0.zip
macOS Binary (x86_64) scde_2.31.0.tgz
macOS Binary (arm64) scde_2.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scde
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scde
Bioc Package Browser https://code.bioconductor.org/browse/scde/
Package Short Url https://bioconductor.org/packages/scde/
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