Package: dominoSignal 1.7.1

Kavita Krishnan

dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing

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 activity (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:Christopher Cherry [aut], Jacob T Mitchell [aut], Sushma Nagaraj [aut], Kavita Krishnan [aut, cre], Dmitrijs Lvovs [aut], Elana Fertig [ctb], Jennifer Elisseeff [ctb]

dominoSignal_1.7.1.tar.gz
dominoSignal_1.7.1.zip(r-4.7-any)dominoSignal_1.7.1.zip(r-4.6-any)dominoSignal_1.7.1.zip(r-4.5-any)
dominoSignal_1.7.1.tgz(r-4.6-any)dominoSignal_1.7.1.tgz(r-4.5-any)
dominoSignal_1.7.1.tar.gz(r-4.7-any)dominoSignal_1.7.1.tar.gz(r-4.6-any)
dominoSignal_1.7.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dominoSignal/json (API)

# Install 'dominoSignal' in R:
install.packages('dominoSignal', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fertiglab/dominosignal/issues

Pkgdown/docs site:https://fertiglab.github.io

Datasets:

On BioConductor:dominoSignal-1.7.0(bioc 3.24)dominoSignal-1.6.0(bioc 3.23)

systemsbiologysinglecelltranscriptomicsnetworksequencing

7.04 score 8 stars 33 scripts 318 downloads 39 exports 129 dependencies

Last updated from:80f2f89695. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE228
linux-develOK361
source / vignettesOK605
linux-releaseOK321
macos-releaseOK286
macos-oldrelOK292
windows-develOK291
windows-releaseOK204
windows-oldrelOK261
wasm-releaseOK166

Exports:add_rl_columnbuild_dominocircos_ligand_receptorcor_heatmapcor_scattercount_linkagecreate_dominocreate_regulon_list_sceniccreate_rl_map_cellphonedbdom_clustersdom_correlationsdom_countsdom_databasedom_dedom_infodom_linkagesdom_network_itemsdom_signalingdom_signallingdom_tf_activationdom_to_dfdom_zscoresfeat_heatmapgene_networkincoming_signaling_heatmapincoming_signalling_heatmapmean_ligand_expressionplot_differential_linkagesprintrename_clustersshowsignaling_heatmapsignaling_networksignalling_heatmapsignalling_networksubsetsummarise_linkagessummarize_linkagestest_differential_linkages

Dependencies:abindAnnotationDbiaskpassbackportsBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbroomcachemcarcarDatacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncurlDBIdbplyrDerivdigestdoBydoParalleldplyrfarverfastmapfilelockforeachforecastFormulafracdiffgenericsGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rjsonrlangRSQLiterstatixS4VectorsS7scalesSeqinfoshapeSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrxml2XVectorzoo

Differential Signaling Workflow
Workflow overview | Demonstration data | The linkage_summary class | Counting linkages across groups | Total counts | Grouped counts | Testing differential linkages | Two-group comparisons | Multi-group comparisons | Visualizing differential linkages | Example run | Related Articles
Rendered fromdifferential_signaling.Rmdusingknitr::rmarkdown

Last update: 2026-10-15
Started: 2026-10-15

Get Started with dominoSignal
Installation | Options and Setup | Data preparation | Loading TF and receptor-ligand data | Loading SCENIC results | Loading the CellPhoneDB database | Optional: Adding interactions manually | Analysis with domino objects | Required inputs from data set | Create domino object | Build the domino network | Visualization of domino results | Summarize TF activity and linkages | Cumulative signaling between clusters | Specific Signaling Interactions between Clusters | Example run | Related articles
Rendered fromdominoSignal.Rmdusingknitr::rmarkdown

Last update: 2026-10-15
Started: 2024-05-08

Interacting with domino Objects
Object contents | Access functions | Input data | Calculations | Linkages | Signaling Matrices | Build information | Related articles
Rendered fromdomino_object_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-10-15
Started: 2023-12-20

Plotting Functions and Options
Setup and data load | Heatmaps | Correlations between receptors and transcription factors | Heatmap of Transcription Factor Activation Scores | Heatmap of incoming signaling for a cluster | Heatmap of signaling between clusters | Network plots | Network showing L-R-TF signaling between clusters | Network showing interaction strength across data | Other types of plots | Chord diagrams connecting ligands and receptors | Scatter plot to visualize correlation | Related articles
Rendered fromplotting_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-10-15
Started: 2023-12-20

Readme and manuals

Help Manual

Help pageTopics
Adds a column to the RL signaling data frame.add_rl_column
Calculate a signaling network for a 'domino()' objectbuild_domino
CellPhoneDB subsetCellPhoneDB
Plot expression of a receptor's ligands by other clusters as a chord plotcircos_ligand_receptor
Create a heatmap of correlation between receptors and transcription factorscor_heatmap
Create a correlation plot between TF and receptorcor_scatter
Count occurrences of linkages across multiple domino results from a linkage summarycount_linkage
Create a 'domino()' object and prepare it for network constructioncreate_domino
Create a list of genes in regulons inferred by SCENICcreate_regulon_list_scenic
Create a receptor-ligand map from a CellPhoneDB signaling databasecreate_rl_map_cellphonedb
Access clustersdom_clusters
Access correlationsdom_correlations
Access countsdom_counts
Access databasedom_database
Access differential expressiondom_de
Access build informationdom_info
Access linkagesdom_linkages
Access all features, receptors, or ligands present in a signaling network.dom_network_items
Access signalingdom_signaling dom_signalling
Access transcription factor activity scoresdom_tf_activation
Turn domino object signaling information into a data framedom_to_df
Access z-scoresdom_zscores
The domino classdomino domino-class
Example domino objectsDominoObjects
Create a heatmap of features organized by clusterfeat_heatmap
Create a gene association networkgene_network
Create a cluster incoming signaling heatmapincoming_signaling_heatmap incoming_signalling_heatmap
The domino linkage summary classlinkage_summary linkage_summary-class
Example linkage summaryLinkageSummary
Calculate mean ligand expression as a data frame for plotting in circos plotmean_ligand_expression
PBMC scRNAseq data subsetPBMC
Plot differential linkages among domino results ranked by a comparative statisticplot_differential_linkages
Print domino objectprint,domino-method
Print linkage summary objectprint,linkage_summary-method
Renames clusters in a 'domino()' objectrename_clusters
SCENIC example subsetSCENIC
Show domino object informationshow,domino-method
Show linkage_summary object informationshow,linkage_summary-method
Create a network heatmapsignaling_heatmap signalling_heatmap
Create a cluster to cluster signaling network diagramsignaling_network signalling_network
Subset a linkage_summary objectsubset,linkage_summary-method
Summarize linkages from multiple domino objectssummarise_linkages summarize_linkages
Statistical test for differential linkages across multiple domino resultstest_differential_linkages