# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "dominoSignal" in publications use:'
type: software
license: GPL-3.0-only
title: 'dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing'
version: 0.99.4
doi: 10.1038/s41551-021-00770-5
abstract: 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.
authors:
- family-names: Cherry
  given-names: Christopher
  email: ccherry.6574@gmail.com
  orcid: https://orcid.org/0000-0002-5481-0055
- family-names: Mitchell
  given-names: Jacob T
  email: jmitch81@jhmi.edu
  orcid: https://orcid.org/0000-0002-5370-9692
- family-names: Nagaraj
  given-names: Sushma
  email: snagara5@jhmi.edu
  orcid: https://orcid.org/0000-0001-5166-1309
- family-names: Krishnan
  given-names: Kavita
  email: kkrishnan@jhmi.edu
  orcid: https://orcid.org/0000-0003-1345-0249
- family-names: Lvovs
  given-names: Dmitrijs
  email: dlvovs1@jhmi.edu
preferred-citation:
  type: article
  title: Computational reconstruction of the signalling networks surrounding implanted
    biomaterials from single-cell transcriptomics
  authors:
  - family-names: Cherry
    given-names: Christopher
    email: ccherry.6574@gmail.com
    orcid: https://orcid.org/0000-0002-5481-0055
  - family-names: Maestas
    given-names: David R.
  - family-names: Han
    given-names: Jin
  - family-names: Andorko
    given-names: James I.
  - family-names: Cahan
    given-names: Patrick
  - family-names: Fertig
    given-names: Elana J.
  - family-names: Garmire
    given-names: Lana X.
  - family-names: Elisseeff
    given-names: Jennifer H.
  journal: Nature Biomedical Engineering
  year: '2021'
  volume: '5'
  issue: '10'
  doi: 10.1038/s41551-021-00770-5
  url: https://doi.org/10.1038%2Fs41551-021-00770-5
  start: 1228-1238
repository: https://bioc.r-universe.dev
repository-code: https://github.com/FertigLab/dominoSignal
commit: 4daf6c500ab7112fb0f77b3749333e0439d15e05
url: https://fertiglab.github.io/dominoSignal/
contact:
- family-names: Mitchell
  given-names: Jacob T
  email: jmitch81@jhmi.edu
  orcid: https://orcid.org/0000-0002-5370-9692
references:
- type: manual
  title: 'dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing'
  authors:
  - family-names: Cherry
    given-names: Christopher
    email: ccherry.6574@gmail.com
    orcid: https://orcid.org/0000-0002-5481-0055
  - family-names: Mitchell
    given-names: Jacob T
    email: jmitch81@jhmi.edu
    orcid: https://orcid.org/0000-0002-5370-9692
  - family-names: Nagaraj
    given-names: Sushma
    email: snagara5@jhmi.edu
    orcid: https://orcid.org/0000-0001-5166-1309
  - family-names: Krishnan
    given-names: Kavita
    email: kkrishnan@jhmi.edu
    orcid: https://orcid.org/0000-0003-1345-0249
  - family-names: Fertig
    given-names: Elana
    email: ejfertig@jhmi.edu
    orcid: https://orcid.org/0000-0003-3204-342X
  - family-names: Elisseeff
    given-names: Jennifer
    email: jhe@jhu.edu
    orcid: https://orcid.org/0000-0002-5066-1996
  year: '2024'
  notes: R package version 0.99.2