Package: COTAN
Type: Package
Title: COexpression Tables ANalysis 
Version: 0.1.0
Author: Silvia Giulia Galfrè, Francesco Morandin, Marco Pietrosanto, Federico Cremisi, Manuela Helmer-Citterich
Maintainer: Silvia Giulia Galfrè <[email protected]>
Description: COTAN is a 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.
Depends: R (>= 3.5.0)
License: CC-BY-ND 4.0
Encoding: UTF-8
RoxygenNote: 7.1.1
Imports:
    dplyr,
    Matrix,
    ggplot2,
    ggrepel,
    data.table,
    parallel,
    tibble,
    dplyr,
    tidyr,
    basilisk,
    reticulate,
    ComplexHeatmap
Suggests: 
    testthat (>= 3.0.0),
    spelling,
    knitr,
    rmarkdown,
    data.table,
    R.utils,
    Matrix,
    dendextend,
    Rtsne,
    plotly,
    tidyverse,
    htmlwidgets,
    MASS
Config/testthat/edition: 3
SystemRequirements: 
    python
Language: en-US
VignetteBuilder: knitr