Package: dominoSignal
Title: Cell Communication Analysis for Single Cell RNA Sequencing
Version: 1.2.0
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, magrittr, purrr,
        dplyr
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/
git_url: https://git.bioconductor.org/packages/dominoSignal
git_branch: RELEASE_3_21
git_last_commit: b090df8
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 00:20:13 UTC; biocbuild
Author: Christopher Cherry [aut] (ORCID:
    <https://orcid.org/0000-0002-5481-0055>),
  Jacob T Mitchell [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5370-9692>),
  Sushma Nagaraj [aut] (ORCID: <https://orcid.org/0000-0001-5166-1309>),
  Kavita Krishnan [aut] (ORCID: <https://orcid.org/0000-0003-1345-0249>),
  Dmitrijs Lvovs [aut],
  Elana Fertig [ctb] (ORCID: <https://orcid.org/0000-0003-3204-342X>),
  Jennifer Elisseeff [ctb] (ORCID:
    <https://orcid.org/0000-0002-5066-1996>)
Maintainer: Jacob T Mitchell <jmitch81@jhmi.edu>
Built: R 4.5.0; ; 2025-04-16 14:21:43 UTC; windows
