Package: scde
Type: Package
Title: Single Cell Differential Expression
Version: 2.39.0
Description: 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]
Authors@R: c(
    person("Peter", "Kharchenko", role = c("aut", "cre"),
             email = "Peter_Kharchenko@hms.harvard.edu"),
    person("Jean", "Fan", role = "aut",
               email = "jeanfan@jhu.edu",     
           comment = c(ORCID = "0000-0002-0212-5451")),
    person("Evan", "Biederstedt", role = "aut",
           email = "evan.biederstedt@gmail.com")
    )
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
URL: http://pklab.med.harvard.edu/scde
BugReports: https://github.com/hms-dbmi/scde/issues
License: GPL-2
LazyData: true
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
Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
        rmarkdown
biocViews: ImmunoOncology, RNASeq, StatisticalMethod,
        DifferentialExpression, Bayesian, Transcription, Software
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Packaged: 2026-03-05 08:57:00 UTC; root
RoxygenNote: 5.0.0
NeedsCompilation: yes
Config/pak/sysreqs: libcairo2-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:28:40 UTC
RemoteUrl: https://github.com/bioc/scde
RemoteRef: HEAD
RemoteSha: 013e4aa8f1b4f767cb52472ea474152bf5e3e81e
Built: R 4.6.0; x86_64-w64-mingw32; 2026-03-05 09:00:08 UTC; windows
Archs: x64
