Package: CiteFuse
Type: Package
Title: CiteFuse: multi-modal analysis of CITE-seq data
Version: 1.25.0
Authors@R: c(
    person("Yingxin", "Lin", email = "yingxin.lin@sydney.edu.au", role = c("aut", "cre")
    ),
    person("Hani", "Kim", email = "jieun.kim@sydney.edu.au", role = c("aut"))
    )
Description: CiteFuse pacakage implements a suite of methods and tools
        for CITE-seq data from pre-processing to integrative analytics,
        including doublet detection, network-based modality
        integration, cell type clustering, differential RNA and protein
        expression analysis, ADT evaluation, ligand-receptor
        interaction analysis, and interactive web-based visualisation
        of the analyses.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
        1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
        dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales,
        scran (>= 1.14.6), graphics, methods, stats, utils, reshape2,
        ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5,
        rlang, Rcpp, compositions
LinkingTo: Rcpp
RoxygenNote: 7.2.3
Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle,
        pkgdown
VignetteBuilder: knitr
LazyData: false
biocViews: SingleCell, GeneExpression
BugReports: https://github.com/SydneyBioX/CiteFuse/issues
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libuv1-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:52:27 UTC
RemoteUrl: https://github.com/bioc/CiteFuse
RemoteRef: HEAD
RemoteSha: 3e1d4c01265cec4bda710eda22f73fee658e5310
NeedsCompilation: yes
Packaged: 2026-06-23 20:22:16 UTC; root
Author: Yingxin Lin [aut, cre],
  Hani Kim [aut]
Maintainer: Yingxin Lin <yingxin.lin@sydney.edu.au>