Package: COTAN
Type: Package
Title: COexpression Tables ANalysis 
Version: 1.2.0
Authors@R: c(
  person("Galfrè", "Silvia Giulia",email = "silvia.galfre@uniroma1.it", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
  person("Morandin","Francesco", email = "francesco.morandin@unipr.it", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
  person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
  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 (>= 4.1)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.2.0
Imports:
    dplyr,
    methods,
    grDevices,
    Matrix,
    ggplot2,
    ggrepel,
    stats,
    parallel,
    tibble,
    tidyr,
    irlba,
    ComplexHeatmap,
    circlize,
    grid,
    scales,
    utils,
    rlang,
    Rfast
Suggests: 
    testthat (>= 3.0.0),
    spelling,
    knitr,
    data.table,
    R.utils,
    tidyverse,
    rmarkdown,
    htmlwidgets,
    MASS,
    factoextra,
    Rtsne,
    plotly,
    dendextend,
    BiocStyle,
    cowplot
Config/testthat/edition: 3
Language: en-US
biocViews: 
    SystemsBiology, 
    Transcriptomics,
    GeneExpression,
    SingleCell
VignetteBuilder: knitr
LazyData: false