Package: dominoSignal 1.1.0

Jacob T Mitchell

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, cre], Sushma Nagaraj [aut], Kavita Krishnan [aut], Dmitrijs Lvovs [aut], Elana Fertig [ctb], Jennifer Elisseeff [ctb]

dominoSignal_1.1.0.tar.gz
dominoSignal_1.1.0.zip(r-4.5)dominoSignal_1.1.0.zip(r-4.4)dominoSignal_1.1.0.zip(r-4.3)
dominoSignal_1.1.0.tgz(r-4.4-any)dominoSignal_1.1.0.tgz(r-4.3-any)
dominoSignal_1.1.0.tar.gz(r-4.5-noble)dominoSignal_1.1.0.tar.gz(r-4.4-noble)
dominoSignal_1.1.0.tgz(r-4.4-emscripten)dominoSignal_1.1.0.tgz(r-4.3-emscripten)
dominoSignal.pdf |dominoSignal.html✨
dominoSignal/json (API)
NEWS

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

Peer review:

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

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

Datasets:

On BioConductor:dominoSignal-1.1.0(bioc 3.21)dominoSignal-1.0.0(bioc 3.20)

systemsbiologysinglecelltranscriptomicsnetwork

6.50 score 3 stars 5 scripts 115 downloads 33 exports 124 dependencies

Last updated 2 months agofrom:865183f370. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

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_summaryplot_differential_linkagesprintrename_clustersshowsignaling_heatmapsignaling_networksummarize_linkagestest_differential_linkages

Dependencies:abindAnnotationDbiaskpassbackportsBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbroomcachemcarcarDatacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncurlDBIdbplyrDerivdigestdoBydoParalleldplyrfansifarverfastmapfilelockforeachFormulagenericsGenomeInfoDbGenomeInfoDbDataGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplogrplyrpngpolynomprettyunitsprogresspurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrjsonrlangRSQLiterstatixS4VectorsscalesshapeSparseMstringistringrsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc

Get Started with dominoSignal

Rendered fromdominoSignal.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-08-05
Started: 2024-05-08

Interacting with domino Objects

Rendered fromdomino_object_vignette.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-07-18
Started: 2023-12-20

Plotting Functions and Options

Rendered fromplotting_vignette.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-07-18
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
Renames clusters in a domino objectrename_clusters
SCENIC AUC subsetSCENIC
Show domino object informationshow,domino-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