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-any)dominoSignal_1.6.0.zip(r-4.6-any)dominoSignal_1.6.0.zip(r-4.5-any)
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

5.50 score 8 stars 28 scripts 318 downloads 35 exports 127 dependencies

Last updated from:c728970521 (on RELEASE_3_23). Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE216
linux-develWARNING417
source / vignettesERROR362
linux-releaseWARNING394
macos-releaseWARNING232
macos-oldrelWARNING206
windows-develWARNING227
windows-releaseWARNING173
windows-oldrelWARNING247
wasm-releaseOK181

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:abindAnnotationDbiaskpassbackportsBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbroomcachemcarcarDatacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncurlDBIdbplyrDerivdigestdoBydoParalleldplyrfarverfastmapfilelockforeachforecastFormulafracdiffgenericsGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrjsonrlangRSQLiterstatixS4VectorsS7scalesSeqinfoshapeSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrxml2XVectorzoo

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