DESCRIPTION

Package: CiteFuse
Type: Package
Title: CiteFuse: multi-modal analysis of CITE-seq data
Version: 1.11.2
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