Package: celda
Title: CEllular Latent Dirichlet Allocation
Version: 1.29.3
Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-0780-8662")),
    person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
    person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut")),
    person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
    person("Yusuke", "Koga", email="ykoga07@bu.edu", role = c("aut")))
Description: Celda is a suite of Bayesian hierarchical models for
        clustering single-cell RNA-sequencing (scRNA-seq) data. It is
        able to perform "bi-clustering" and simultaneously cluster
        genes into gene modules and cells into cell subpopulations. It
        also provides wrapper functions for DecontX, a Bayesian method
        to computationally estimate and remove RNA contamination in
        individual cells without empty droplet information, which is
        implemented in the 'decontX' package. A variety of scRNA-seq
        data visualization functions is also included.
Depends: R (>= 4.5.0), SingleCellExperiment, Matrix
VignetteBuilder: knitr
Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
        grDevices, graphics, matrixStats, doParallel, digest, methods,
        reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot,
        enrichR, SummarizedExperiment, ggrepel, Rtsne, withr, dbscan,
        stringr, ComplexHeatmap, gridExtra, circlize, dendextend,
        ggdendro, pROC
Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
        BiocManager, BiocStyle, TENxPBMCData, singleCellTK,
        M3DExampleData, decontX, scater, Seurat
LinkingTo: Rcpp, RcppEigen
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
URL: https://github.com/campbio/celda, https://www.camplab.net/celda
BugReports: https://github.com/campbio/celda/issues
biocViews: SingleCell, GeneExpression, Clustering, Sequencing,
        Bayesian, ImmunoOncology, DataImport
NeedsCompilation: yes
RoxygenNote: 7.3.2
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-09 20:27:27 UTC
RemoteUrl: https://github.com/bioc/celda
RemoteRef: HEAD
RemoteSha: 7dd371780aa32513052ff225860d4664f3d7fdf6
Packaged: 2026-10-10 01:12:52 UTC; root
Author: Joshua Campbell [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0780-8662>),
  Shiyi Yang [aut],
  Zhe Wang [aut],
  Sean Corbett [aut],
  Yusuke Koga [aut]
Maintainer: Joshua Campbell <camp@bu.edu>