Package: dominoSignal 1.6.0

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

dominoSignal_1.6.0.tar.gz
dominoSignal_1.6.0.zip(r-4.7)dominoSignal_1.6.0.zip(r-4.6)dominoSignal_1.6.0.zip(r-4.5)
dominoSignal_1.6.0.tgz(r-4.6-any)dominoSignal_1.6.0.tgz(r-4.5-any)
dominoSignal_1.6.0.tar.gz(r-4.7-any)dominoSignal_1.6.0.tar.gz(r-4.6-any)
dominoSignal_1.6.0.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-release.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)

systemsbiologysinglecelltranscriptomicsnetwork

6.92 score 7 stars 28 scripts 35 exports 128 dependencies

Last updated from:c728970521 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE259
linux-devel-x86_64OK359
source / vignettesOK378
linux-release-x86_64OK344
macos-release-arm64OK175
macos-oldrel-arm64OK164
windows-develOK236
windows-releaseOK219
windows-oldrelOK242
wasm-releaseOK228

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_tf_activationdom_zscoresfeat_heatmapgene_networkincoming_signaling_heatmapmean_ligand_expressionmock_linkage_summaryobtain_circos_expressionplot_differential_linkagesprintrename_clustersrender_circos_ligand_receptorshowsignaling_heatmapsignaling_networksummarize_linkagestest_differential_linkages

Dependencies:abindAnnotationDbiaskpassbackportsBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbroomcachemcarcarDatacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncurlDBIdbplyrDerivdigestdoBydoParalleldplyrfarverfastmapfilelockforeachforecastFormulafracdiffgenericsGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogresspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrjsonrlangRSQLiterstatixS4VectorsS7scalesSeqinfoshapeSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrxml2XVectorzoo

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 | Continued Development
Rendered fromplotting_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2023-12-20

Get Started with dominoSignal
Options and Setup | Data preparation | Installation | Loading TF and R - L data | Loading SCENIC Results | Load CellPhoneDB Database | Optional: Adding interactions manually | Analysis with Domino object | Required inputs from data set | Create Domino object | Build Domino Network | Visualization of Domino Results | Summarize TF Activity and Linkage | Cumulative signaling between cell types | Specific Signaling Interactions between Clusters | Continued Development
Rendered fromdominoSignal.Rmdusingknitr::rmarkdown

Last update: 2026-04-14
Started: 2024-05-08

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

Last update: 2026-04-13
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 cell types 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
Access transcription factor activationdom_tf_activation
Access z-scoresdom_zscores
The domino classdomino domino-class
Create a heatmap of features organized by clusterfeat_heatmap
Create a gene association networkgene_network
Create a cluster incoming signaling heatmapincoming_signaling_heatmap
The domino linkage summary classlinkage_summary linkage_summary-class
Calculate mean ligand expression as a data frame for plotting in circos plotmean_ligand_expression
Create a mock linkage summary objectmock_linkage_summary
PBMC RNAseq 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 AUC subsetSCENIC
Show domino object informationshow,domino-method
Show linkage_summary object informationshow,linkage_summary-method
Create a network heatmapsignaling_heatmap
Create a cluster to cluster signaling network diagramsignaling_network
Summarize linkages from multiple domino objectssummarize_linkages
Statistical test for differential linkages across multiple domino resultstest_differential_linkages