Package: clustifyr
Title: Classifier for Single-cell RNA-seq Using Cell Clusters
Version: 1.22.0
Description: Package designed to aid in classifying cells from
        single-cell RNA sequencing data using external reference data
        (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A
        variety of correlation based methods and gene list enrichment
        methods are provided to assist cell type assignment.
Authors@R: 
    c(person(given = "Rui",
             family = "Fu",
             role = c("cre", "aut"), 
             email = "ray.sinensis@gmail.com"),
      person(given = "Kent",
             family = "Riemondy",
             role =  "aut",
             email = "kent.riemondy@gmail.com"),
      person(given = "Austin",
             family = "Gillen",
             role = "ctb",
             email = "austin.gillen@ucdenver.edu"),
      person(given = "Chengzhe",
             family = "Tian",
             role = "ctb",
             email = "Chengzhe.Tian@colorado.edu"),
      person(given = "Jay",
             family = "Hesselberth",
             role = "ctb",
             email = "jay.hesselberth@gmail.com"),
      person(given = "Yue",
             family = "Hao",
             role = "ctb",
             email = "haoyuethink@gmail.com"),
      person(given = "Michelle",
             family = "Daya",
             role = "ctb",
             email = "michelle.daya@ucdenver.edu"),
      person(given = "Sidhant",
             family = "Puntambekar",
             role = "ctb",
             email = "sidhantnp@yahoo.com"),
      person("RNA Bioscience Initiative", role = c("fnd", "cph"),
           comment = c(ROR = "https://ror.org/03wmf1y16"))
      )
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang,
        scales, stringr, tibble, tidyr, stats, methods,
        SingleCellExperiment, SummarizedExperiment, SeuratObject,
        matrixStats, S4Vectors, proxy, httr, utils
Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
        BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr,
        data.table, R.utils
biocViews: SingleCell, Annotation, Sequencing, Microarray,
        GeneExpression
BugReports: https://github.com/rnabioco/clustifyr/issues
URL: https://github.com/rnabioco/clustifyr,
        https://rnabioco.github.io/clustifyr/
VignetteBuilder: knitr
ByteCompile: true
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
LazyData: true
Config/Needs/website: pkgdown, rnabioco/rbitemplate
Config/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:56:51 UTC
RemoteUrl: https://github.com/bioc/clustifyr
RemoteRef: RELEASE_3_22
RemoteSha: 9338c89f0bafc4de66db32505c2b1c389770bd62
NeedsCompilation: no
Packaged: 2026-01-28 07:19:31 UTC; root
Author: Rui Fu [cre, aut],
  Kent Riemondy [aut],
  Austin Gillen [ctb],
  Chengzhe Tian [ctb],
  Jay Hesselberth [ctb],
  Yue Hao [ctb],
  Michelle Daya [ctb],
  Sidhant Puntambekar [ctb],
  RNA Bioscience Initiative [fnd, cph] (ROR: <https://ror.org/03wmf1y16>)
Maintainer: Rui Fu <ray.sinensis@gmail.com>
Built: R 4.5.2; ; 2026-01-28 07:22:20 UTC; windows
