Changelog

Source: NEWS.md

scMetaLink 0.99.1

Bug Fixes and Improvements

• Added createScMetaLinkFromSCE() function for SingleCellExperiment support
• Cleaned repository structure for Bioconductor submission
• Reduced package size by optimizing vignettes

scMetaLink 0.99.0

New Features

• Initial Bioconductor submission
• createScMetaLink() - Create scMetaLink object from expression data
• createScMetaLinkFromSeurat() - Create from Seurat object
• createScMetaLinkFromSCE() - Create from SingleCellExperiment
• createScMetaLinkFromSpatial() - Create from spatial transcriptomics data
• inferProduction() - Infer metabolite production potential
• inferSensing() - Infer metabolite sensing capability
• computeCommunication() - Compute cell-cell communication scores
• computeSpatialCommunication() - Spatial communication analysis
• filterSignificantInteractions() - Filter by statistical significance
• aggregateByPathway() - Pathway-level aggregation

Lactate Signaling Module

• inferLactateSignaling() - Specialized lactate communication analysis
• checkLactateGenes() - Check lactate-related gene availability
• getLactateGenes() - Get curated lactate gene sets

Visualization

• plotCommunicationHeatmap() - Communication heatmap
• plotCommunicationCircle() - Chord diagram
• plotCommunicationNetwork() - Network visualization
• plotMetaboliteFlow() - Metabolite flow diagram
• plotSpatialCellTypes() - Spatial cell type distribution
• plotSpatialFeature() - Spatial feature maps
• plotSpatialCommunicationNetwork() - Spatial network overlay