DESCRIPTION

Package: dominoSignal
Title: Cell Communication Analysis for Single Cell RNA Sequencing
Version: 1.0.1
Authors@R: c(
    person("Christopher", "Cherry", role = c("aut"), email = "ccherry.6574@gmail.com", comment = c(ORCID = "0000-0002-5481-0055")),
    person("Jacob T", "Mitchell", role = c("aut", "cre"), email = "jmitch81@jhmi.edu", comment = c(ORCID = "0000-0002-5370-9692")),
    person("Sushma", "Nagaraj", role = c("aut"), email = "snagara5@jhmi.edu", comment = c(ORCID = "0000-0001-5166-1309")),
    person("Kavita", "Krishnan", role = c("aut"), email = "kkrishnan@jhmi.edu", comment = c(ORCID = "0000-0003-1345-0249")),
    person("Dmitrijs", "Lvovs", role = c("aut"), email = "dlvovs1@jhmi.edu"),
    person("Elana", "Fertig", role = "ctb", email = "ejfertig@jhmi.edu", comment = c(ORCID = "0000-0003-3204-342X")),
    person("Jennifer", "Elisseeff", role = "ctb", email = "jhe@jhu.edu", comment = c(ORCID = "0000-0002-5066-1996"))
    )
Description: 
    dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
BugReports: https://github.com/FertigLab/dominoSignal/issues
Depends:
    R(>= 4.2.0),
Imports:
    biomaRt,
    ComplexHeatmap,
    circlize,
    ggpubr,
    grDevices,
    grid,
    igraph,
    Matrix,
    methods,
    plyr,
    stats,
    utils
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
biocViews:
    SystemsBiology,
    SingleCell,
    Transcriptomics,
    Network
Suggests:
    knitr,
    patchwork,
    rmarkdown,
    Seurat,
    testthat,
    formatR,
    BiocFileCache,
    SingleCellExperiment
VignetteBuilder: knitr
Language: en-US
Roxygen: list(markdown = TRUE)
URL: https://fertiglab.github.io/dominoSignal/