Flufftail/DESCRIPTION at main · Core-Bioinformatics/Flufftail · GitHub

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Package: Flufftail
Title: A package for the analysis of single-cell data using fuzzy clustering
Version: 0.0.1
Authors@R:
    person(given="Rafael", family="Kollyfas", email="rk720@cam.ac.uk", role = c("aut", "cre"))
Description: Provides tools for single-cell data analysis using fuzzy clustering.
    The package introduces a fuzzy community-detection framework that captures
    the variability of standard clustering methods and characterizes fuzzy entries
    such as cells and genes. It enables the assessment of membership degrees,
    characterisation of hard clusters, and evaluation of co-clustering behaviour,
    all summarised in interactive visualisations that promote communication between
    wet- and dry-lab researchers. A novel methodology is included for identifying
    key regulatory genes that drive biological transitions through fuzzy gene
    module clustering. The package also offers a new approach for characterising
    gene regulatory network (GRN) dynamics and tracing the evolution of regulatory
    interactions among major regulatory hub genes across pseudotime.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports:
    shiny,
    readr,
    tidyr,
    shinythemes,
    DT,
    plotly,
    pheatmap,
    shinyjs,
    viridis,
    Seurat,
    patchwork,
    uwot,
    tidyverse,
    reticulate,
    dplyr,
    visNetwork,
    ggforce,
    data.table,
    cowplot,
    RcppEigen,
    parallel,
    ClustAssess,
    ggplot2,
    stringr,
    clue,
    gprofiler2,
    Matrix,
    methods,
    DelayedMatrixStats,
    Gmedian,
    SingleCellExperiment,
    assertthat,
    igraph,
    plyr,
    reshape2
LinkingTo: Rcpp, RcppEigen
Suggests:
    monocle3,
    SeuratWrappers
Config/testthat/edition: 3