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Key features\ninclude probabilistic inference of metabolite production,\nreceptor-mediated metabolite sensing quantification,\npermutation-based statistical testing with multiple hypothesis\ncorrection, pathway-level aggregation analysis, and\npublication-ready visualization.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "VignetteBuilder": "knitr", "biocViews": "Software, SingleCell, Transcriptomics, CellBiology,\nMetabolomics, Network, Visualization, GeneExpression, Spatial", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "URL": "https://github.com/Zaoqu-Liu/scMetaLink,\nhttps://Zaoqu-Liu.github.io/scMetaLink/", "BugReports": "https://github.com/Zaoqu-Liu/scMetaLink/issues", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libpng-dev libxml2-dev perl", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-26 15:42:34 UTC", "RemoteUrl": 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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" ], "created": "2026-01-22 03:14:49", "modified": "2026-01-22 03:20:29", "commits": 2 }, { "source": "theory.Rmd", "filename": "theory.html", "title": "Theory & Methods", "engine": "knitr::rmarkdown", "headings": [ "Overview", "The MetalinksDB Knowledge Base", "Interaction Types", "Mode of Regulation (MOR)", "Protein Types", "Mathematical Framework", "1. 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Population Size Correction (Optional)", "Statistical Framework", "Permutation Test", "Multiple Testing Correction", "Data Processing Pipeline", "Key Assumptions", "Comparison with Ligand-Receptor Methods", "References", "Next" ], "created": "2026-01-22 03:14:49", "modified": "2026-01-22 03:20:29", "commits": 2 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "scmetalink", "_universes": [ "zaoqu-liu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-05-28T10:59:08.000Z", "distro": "noble", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "ff3169e1e94a31ad2c7dd8128552a0ce5c6b1bac1f601ac1fbb3a9e3bc8d0409", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.6.0", "os": "linux", "version": "0.99.1", "date": "2026-05-28T10:58:49.000Z", "distro": "noble", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "51dd2fa65aaf03eb4a77e1a6c77fee4ebb4a8cd4d95291dfc726fb1bb73b9114", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-05-28T10:57:44.000Z", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "8de39ee9853866e5bd18681491bec88113579c617aa9e311f95f6b0f420e0e5c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.6.0", "os": "mac", "version": "0.99.1", "date": "2026-05-28T10:57:58.000Z", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "a2346854360d34b0e64a5fd5c730b91c766814d05ec3800cbe4ea5e4abdd83f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.1", "date": "2026-05-28T10:58:44.000Z", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "271c0c6a1b3bb0d0c4879d2a57588f296f07fae02aa53744d2b624f106e6edf8", "status": "success", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-05-28T10:57:37.000Z", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "3b3a88a7628a1e08212c6f83331ad0b7086e2fd1e21fe4475f650703261f5ab9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.5.3", "os": "win", "version": "0.99.1", "date": "2026-05-28T10:57:43.000Z", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "11f36f1e05a62444a67a33788d9c1fbd0fc54c320cb416196bc2a2d541a591ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" }, { "r": "4.6.0", "os": "win", "version": "0.99.1", "date": "2026-05-28T10:57:45.000Z", "commit": "d5e03bd61e72741e7fce77da7980a68261c230e3", "fileid": "3f3a4ddebbe09ea24f2a7d206bf8d3efae95675b9eec4cde769883c3b1c00970", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26570219392" } ] }