DESCRIPTION

Package: CytoTalk
Title: Signal Transduction Networks from scRNA-seq
Version: 0.99.9
Depends: R (>= 4.1.0)
Authors@R: c(
    person("Yuxuan", "Hu",
		   role = c("aut"),
		   comment = c(ORCID = "0000-0002-8830-6893")),
    person("Shane", "Drabing",
		   role = c("aut"),
           comment = c(ORCID = "0000-0001-9521-6610")),
    person("Kai", "Tai",
		   role = c("cre"),
	       email = "tanlab4generegulation@gmail.com",
		   comment = c(ORCID = "0000-0002-9104-5567")))
Description: Perform de novo construction of signal transduction networks using
	single-cell transcriptomic data (scRNA-seq). The CytoTalk process
	constructs an integrated network of intra- and inter-cellular functional
	gene interactions, generating useful graphical output for investigation of
	cell-cell communication within and between cell types. CytoTalk attempts to
	find the optimal subnetwork in the integrated network that includes genes
	with high levels of cell-type-specific expression and close connection to
	highly active ligand-receptor pairs. It takes into account metrics like as
	Preferential Expression Measure (PEM), mutual information between proteins,
	gene relevance, and non-self-talk score.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Imports:
    DiagrammeR,
    DiagrammeRsvg,
    Matrix,
    corpcor,
    doParallel,
    foreach,
    infotheo,
    parmigene,
    reticulate,
    SingleCellExperiment,
    tibble,
    vroom
Suggests: 
    markdown,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Software, SingleCell, GeneExpression, Network, Pathways
SystemRequirements:
	Cytoscape,
	Graphviz,
	pcst_fast
Config/testthat/edition: 3