Package: COTAN
Type: Package
Title: COexpression Tables ANalysis 
Version: 2.9.5
Authors@R: c(
  person("Galfrè", "Silvia Giulia",email = "[email protected]", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
  person("Morandin","Francesco", email = "[email protected]", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
  person("Fantozzi", "Marco", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-0708-5495")),
  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
  person("Puttini","Daniel", role = "aut", comment = c(ORCID = "0009-0006-8401-9949")),
  person("Priami","Corrado", role = "aut", comment = c(ORCID = "0000-0002-3261-6235")),
  person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
  person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504"))
  )
Description: Statistical and computational method to analyze the co-expression of 
    gene pairs at single cell level. It provides the foundation for single-cell gene 
    interactome analysis. The basic idea is studying the zero UMI counts' distribution 
    instead of focusing on positive counts; this is done with a generalized contingency 
    tables framework. COTAN can effectively assess the correlated or anti-correlated 
    expression of gene pairs. It provides a numerical index related to the correlation and an 
    approximate p-value for the associated independence test. COTAN can also evaluate whether 
    single genes are differentially expressed, scoring them with a newly defined global 
    differentiation index. Moreover, this approach provides ways to plot and cluster genes
    according to their co-expression pattern with other genes, effectively helping the study 
    of gene interactions and becoming a new tool to identify cell-identity marker genes.
URL: https://github.com/seriph78/COTAN
BugReports: https://github.com/seriph78/COTAN/issues
Depends: R (>= 4.3)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Imports:
    stats,
    methods,
    grDevices,
    Matrix,
    ggplot2,
    ggrepel,
    gghalves,
    ggthemes,
    graphics,
    parallel,
    parallelly,
    tibble,
    tidyr,
    dplyr,
    BiocSingular,
    parallelDist,
    ComplexHeatmap,
    circlize,
    grid,
    scales,
    RColorBrewer,
    utils,
    rlang,
    Rfast,
    stringr,
    Seurat,
    dendextend,
    zeallot,
    assertthat,
    withr,
    SingleCellExperiment,
    proxy,
    RSpectra
Suggests: 
    testthat (>= 3.2.0),
    proto,
    spelling,
    knitr,
    data.table,
    gsubfn,
    R.utils,
    tidyverse,
    rmarkdown,
    htmlwidgets,
    MASS,
    Rtsne,
    plotly,
    BiocStyle,
    cowplot,
    qpdf,
    GEOquery,
    sf,
    torch,
    SummarizedExperiment,
    S4Vectors
Config/testthat/edition: 3
Language: en-US
biocViews: 
    SystemsBiology, 
    Transcriptomics,
    GeneExpression,
    SingleCell
VignetteBuilder: knitr
LazyData: false