Package index • scMetaLink

All functions
`getProductionScores()` `getSensingScores()` `getCommunicationScores()` `getSignificantInteractions()` `getPathwayAggregated()` `getParameters()`	Accessor Functions for scMetaLink Objects
`aggregateByPathway()`	Aggregate Communication by Pathway
`checkLactateGenes()`	Check Lactate Gene Availability
`citationScMetaLink()`	Show Package Citation
`compareCommunication()`	Compare Two Conditions
`computeCommunication()`	Compute Metabolite-Mediated Cell Communication
`computeSpatialCommunication()`	Compute Spatial Communication
`crc_expr`	CRC Example Expression Data
`crc_meta`	CRC Example Cell Metadata
`createScMetaLink()`	Create scMetaLink Object
`createScMetaLinkFromSCE()`	Create scMetaLink from SingleCellExperiment
`createScMetaLinkFromSeurat()`	Create scMetaLink from Seurat Object
`createScMetaLinkFromSeuratSpatial()`	Create scMetaLink from Seurat Spatial Object
`createScMetaLinkFromSpatial()`	Create scMetaLink Object from Spatial Data
`enrichPathways()`	Pathway Enrichment Analysis
`exportResults()`	Export Results to CSV
`filterSignificantInteractions()`	Filter Significant Interactions
`getCommunicationMatrix()`	Get Communication Summary Matrix
`getDatabaseInfo()`	Get Database Information
`getLactateGenes()`	Get Lactate Signaling Gene Sets
`getLactateSignalingSummary()`	Get Lactate Signaling Summary
`getMetaboliteReceptors()`	Get Receptors for a Metabolite
`getPathwayCommunicationMatrix()`	Get Pathway Communication Matrix
`getPathwayMetaboliteNetwork()`	Get Pathway-Metabolite Network
`getPathwayMetabolites()`	Get Metabolites in Pathway
`getSpatialDistanceStats()`	Get Spatial Distance Statistics
`getSpatialLactateHotspots()`	Get Spatial Lactate Hotspots
`getSummaryStats()`	Get Summary Statistics
`getTopLactateProducers()`	Get Top Lactate Producers
`getTopLactateSensors()`	Get Top Lactate Sensors
`getTopProducers()`	Get Top Producing Cell Types for a Metabolite
`getTopSensors()`	Get Top Sensing Cell Types for a Metabolite
`identifyCellTypeSpecificMetabolites()`	Identify Cell Type Specific Metabolites
`identifyCommunicationHotspots()`	Identify Communication Hotspots
`inferLactateSignaling()`	Infer Lactate-Mediated Cell Communication
`inferProduction()`	Infer Metabolite Production Potential
`inferSensing()`	Infer Metabolite Sensing Capability
`inferSpatialLactateSignaling()`	Infer Spatial Lactate Signaling
`listGenes()`	List Available Genes
`listMetabolites()`	List Available Metabolites
`listTopPathways()`	List Top Pathways
`loadScMetaLink()`	Load scMetaLink Object
`metalinksdb`	MetalinksDB Database
`plotCommunicationCircle()`	Plot Communication Circle
`plotCommunicationHeatmap()`	Plot Communication Heatmap
`plotCommunicationNetwork()`	Plot Communication Network
`plotDifferentialCommunication()`	Plot Differential Communication
`plotEnrichedPathways()`	Plot Enriched Pathways
`plotLactatePathwayComparison()`	Plot Lactate Pathway Comparison
`plotLactateSignaling()`	Plot Lactate Signaling Heatmap
`plotMetaboliteProfile()`	Plot Metabolite Profile
`plotPathwayCommunication()`	Plot Pathway Communication
`plotSpatialCellTypes()`	Plot Spatial Cell Types
`plotSpatialCommunicationNetwork()`	Plot Spatial Communication Network
`plotSpatialComparison()`	Plot Spatial Communication Comparison
`plotSpatialDistanceDistribution()`	Plot Spatial Distance Distribution
`plotSpatialFeature()`	Plot Spatial Communication Heatmap
`plotSpatialHotspots()`	Plot Spatial Hotspots
`plotSpatialLactate()`	Plot Spatial Lactate Signaling
`plotTopInteractions()`	Plot Top Interactions
`runScMetaLink()`	Run Complete scMetaLink Analysis
`runScMetaLinkSeurat()`	Run scMetaLink from Seurat Object
`saveScMetaLink()`	Save scMetaLink Object
`show(<scMetaLink>)`	scMetaLink Class Definition
`scMetaLink` `scMetaLink-package`	scMetaLink: Single-Cell Metabolite-Mediated Cell Communication Analysis
`searchGene()`	Search Gene in Database
`searchMetabolite()`	Search Metabolite in Database
`st_expr`	Colon Spatial Transcriptomics Expression Data
`st_meta`	Colon Spatial Transcriptomics Metadata
`st_scalefactors`	Colon Spatial Transcriptomics Scale Factors
`summarizeCommunicationPairs()`	Summarize Communication by Cell Type Pairs
`summarizePathwayActivity()`	Summarize Pathway Activity

Reference

All functions