Introduction | What You'll Learn | Installation | Load Package and Example Data | The 5-Minute Workflow | Step 1: Create scMetaLink Object | Step 2: Infer Metabolite Production | Step 3: Infer Metabolite Sensing | Step 4: Compute Communication | Step 5: Filter Significant Interactions | Quick Visualization | Communication Heatmap | Chord Diagram | One-Line Workflow | Understanding the Output | Key Objects in the Result | Accessing Results | Export Results | Next Steps | Session Info
Package: scMetaLink 0.99.1
scMetaLink: Single-Cell Metabolite-Mediated Cell Communication Analysis
A comprehensive framework for inferring metabolite-mediated cell-cell communication from single-cell transcriptomic data. scMetaLink integrates metabolite production potential via enzyme expression, metabolite sensing capability via receptor and transporter expression, and secretion potential to construct intercellular metabolic communication networks. The package leverages the MetalinksDB database containing 41894 metabolite-protein interactions covering 1128 metabolites and 4374 proteins. Key features include probabilistic inference of metabolite production, receptor-mediated metabolite sensing quantification, permutation-based statistical testing with multiple hypothesis correction, pathway-level aggregation analysis, and publication-ready visualization.
Authors:
scMetaLink_0.99.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scMetaLink/json (API)
| # Install 'scMetaLink' in R: |
| install.packages('scMetaLink', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zaoqu-liu/scmetalink/issues
Pkgdown/docs site:https://zaoqu-liu.github.io
Datasets:
- crc_expr - CRC Example Expression Data
- crc_meta - CRC Example Cell Metadata
- metalinksdb - MetalinksDB Database
- st_expr - Colon Spatial Transcriptomics Expression Data
- st_meta - Colon Spatial Transcriptomics Metadata
- st_scalefactors - Colon Spatial Transcriptomics Scale Factors
softwaresinglecelltranscriptomicscellbiologymetabolomicsnetworkvisualizationgeneexpressionspatial
Last updated from:d5e03bd61e. Checks:7 NOTE, 2 OK. Indexed: yes.
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| linux-devel-x86_64 | NOTE | 262 | ||
| source / vignettes | OK | 323 | ||
| linux-release-x86_64 | NOTE | 240 | ||
| macos-release-arm64 | NOTE | 181 | ||
| macos-oldrel-arm64 | NOTE | 163 | ||
| windows-devel | NOTE | 180 | ||
| windows-release | NOTE | 181 | ||
| windows-oldrel | NOTE | 179 | ||
| wasm-release | OK | 173 |
Exports:aggregateByPathwaycheckLactateGenescitationScMetaLinkcompareCommunicationcomputeCommunicationcomputeSpatialCommunicationcreateScMetaLinkcreateScMetaLinkFromSCEcreateScMetaLinkFromSeuratcreateScMetaLinkFromSeuratSpatialcreateScMetaLinkFromSpatialenrichPathwaysexportResultsfilterSignificantInteractionsgetCommunicationMatrixgetCommunicationScoresgetDatabaseInfogetLactateGenesgetLactateSignalingSummarygetMetaboliteReceptorsgetParametersgetPathwayAggregatedgetPathwayCommunicationMatrixgetPathwayMetaboliteNetworkgetPathwayMetabolitesgetProductionScoresgetSensingScoresgetSignificantInteractionsgetSpatialDistanceStatsgetSpatialLactateHotspotsgetSummaryStatsgetTopLactateProducersgetTopLactateSensorsgetTopProducersgetTopSensorsidentifyCellTypeSpecificMetabolitesidentifyCommunicationHotspotsinferLactateSignalinginferProductioninferSensinginferSpatialLactateSignalinglistGeneslistMetaboliteslistTopPathwaysloadScMetaLinkplotCommunicationCircleplotCommunicationHeatmapplotCommunicationNetworkplotDifferentialCommunicationplotEnrichedPathwaysplotLactatePathwayComparisonplotLactateSignalingplotMetaboliteProfileplotPathwayCommunicationplotSpatialCellTypesplotSpatialCommunicationNetworkplotSpatialComparisonplotSpatialDistanceDistributionplotSpatialFeatureplotSpatialHotspotsplotSpatialLactateplotTopInteractionsrunScMetaLinkrunScMetaLinkSeuratsaveScMetaLinksearchGenesearchMetaboliteshowsummarizeCommunicationPairssummarizePathwayActivity
Dependencies:base64encBiocGenericscachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondigestdoParalleldplyrfarverfastmapforeachfuturefuture.applygenericsGetoptLongggforceggplot2ggraphggrepelGlobalOptionsglobalsgluegraphlayoutsgridExtragtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmemoiseparallellypillarpkgconfigpngpolyclippurrrR6RColorBrewerRcppRcppArmadillorjsonrlangS4VectorsS7scalesshapestringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr
Quick Start Guide
Last update: 2026-01-22
Started: 2026-01-22
Theory & Methods
Overview | The MetalinksDB Knowledge Base | Interaction Types | Mode of Regulation (MOR) | Protein Types | Mathematical Framework | 1. Metabolite Production Potential (MPP) | Gene Expression Scoring | Trimean Option | 2. Metabolite Sensing Capability (MSC) | Affinity Weighting | Hill Function (Optional) | 3. Communication Score | 4. Population Size Correction (Optional) | Statistical Framework | Permutation Test | Multiple Testing Correction | Data Processing Pipeline | Key Assumptions | Comparison with Ligand-Receptor Methods | References | Next
Last update: 2026-01-22
Started: 2026-01-22
