DESCRIPTION

Package: ClusterDE
Title: A Post-clustering Differential Expression (DE) Method For Solving Double Dipping
Version: 0.99.3
Authors@R:
    c(person("Dongyuan", "Song", , "dongyuansong@ucla.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-1114-1215")),
    person("Kexin", "Li", , "aileenlikexin@outlook.com",  role = c("aut"),
           comment = c(ORCID = "0000-0002-4955-3832")),
    person("Siqi", "Chen", , "siqichen4477@gmail.com",  role = c("aut"),
           comment = c(ORCID = "0000−0002−4955−3832")))
Description: ClusterDE is a post-clustering DE method for controlling the false discovery rate (FDR) of identified DE genes regardless of clustering quality. The core idea of ClusterDE is to generate real-data-based synthetic null data with only one cluster, as a counterfactual in contrast to the real data, for evaluating the whole procedure of clustering followed by a DE test.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.2.0)
Imports: scDesign3,
         SummarizedExperiment,
         SingleCellExperiment,
         dplyr,
         PairedData,
         MASS,
         fitdistrplus,
         rvinecopulib,
         Matrix,
         mvnfast,
         matrixStats,
         methods,
         pbmcapply,
         coop,
         scales
Suggests: parallel,
          ggplot2,
          knitr,
          rmarkdown,
          testthat (>= 3.0.0),
          RefManageR,
          sessioninfo,
          BiocStyle,
          patchwork,
          tools,
          Seurat,
          ape,
          BayesSpace,
          spatialLIBD,
          ape
Remotes: SONGDONGYUAN1994/scDesign3
biocViews:
         Software,
         SingleCell,
         Clustering
URL: https://github.com/SONGDONGYUAN1994/ClusterDE, https://songdongyuan1994.github.io/ClusterDE/
BugReports: https://github.com/SONGDONGYUAN1994/ClusterDE/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr