{ "_id": "6a1f1afab401979e7341f30a", "Package": "SmCCNet", "Title": "Sparse Multiple Canonical Correlation Network Analysis Tool\n('SmCCNet')", "Version": "2.0.7", "Date": "2026-04-30", "Authors@R": "c(person(given = \"Abhinav\",\nfamily = \"Pundir\",\nrole = \"cre\",\nemail=\"abhinav.pundir@ucdenver.edu\"),\nperson(given = \"Weixuan\",\nfamily = \"Liu\",\nrole = \"aut\",\nemail = \"weixuan.liu@cuanschutz.edu\"),\nperson(given = \"Yonghua\",\nfamily = \"Zhuang\",\nrole = \"aut\"),\nperson(given = c(\"W.\", \"Jenny\"),\nfamily = \"Shi\",\nrole = \"aut\"),\nperson(given = \"Thao\",\nfamily = \"Vu\",\nrole = \"aut\"),\nperson(given = \"Iain\",\nfamily = \"Konigsberg\",\nrole = \"aut\"),\nperson(given = \"Katherine\",\nfamily = \"Pratte\",\nrole = \"aut\"),\nperson(given = \"Laura\",\nfamily = \"Saba\",\nrole = \"aut\"),\nperson(given = \"Katerina\",\nfamily = \"Kechris\",\nrole = \"aut\"))", "Description": "A canonical correlation based framework ('SmCCNet')\ndesigned for the construction of phenotype-specific multi-omics\nnetworks. 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Preprocessing", "Step II: Determine optimal sparsity penalties through cross-validation (optional)", "Create test and training data sets.", "Set Scaling Factors", "Run K-fold CV", "Extract penalty pair with the smallest total prediction error", "Step III: Run SmCCA with pre-selected penalty term", "Step IV: Obtain multi-omics modules through network clustering", "Step V: Obtain network summarization score and pruned subnetworks", "Results", "Step VI: Visualize network module", "Methods for Optimal Scaling Factors Selection", "Method 1: Use Prompt to Define Scaling Factors", "Method 2: Use Automated SmCCNet to Select Scaling Factors Based on Pairwise Correlation.", "Method 3: Use Cross-Validation to Select Scaling Factors", "Cross validation with each set of scaling factors", "Select optimal scaling factors with associated penalty parameters", "Multi-Omics SmCCNet with Binary Phenotype", "Extract penalty terms with the highest testing evaluation score", "Step III: Run SPLSDA with pre-selected penalty terms", "Acknowledgments", "Session info", "References" ], "created": "2023-10-03 23:06:06", "modified": "2026-05-08 16:43:25", "commits": 4 }, { "source": "SmCCNet_Vignette_SingleOmics.Rmd", "filename": "SmCCNet_Vignette_SingleOmics.html", "title": "Reconstructing Phenotype-Specific Single-Omics Networks with SmCCNet", "author": "Weixuan Liu, Katerina Kechris", "engine": "knitr::rmarkdown", "headings": [ "SmCCNet package", "SmCCNet single-omics workflow with a synthetic dataset", "Step I. Preprocessing", "Step II: Determine optimal sparsity penalties through cross-validation (optional)", "Create test and training data sets.", "Run K-fold Cross-Validation", "Extract penalty term with the smallest total prediction error", "Step III: Run SmCCA with pre-selected penalty term", "Step IV: Obtain single-omics modules through network clustering", "Step V: Obtain network summarization score and pruned subnetworks", "Results", "Step VI: Visualize network module", "Single-omics SmCCNet for Binary Phenotype", "Import synthetic dataset with binary phenotype", "Step II: Determine optimal sparsity penalty through cross-validation (optional)", "Step III: Run SPLSDA with pre-selected penalty term", "Session info", "References" ], "created": "2023-10-03 23:06:06", "modified": "2026-05-08 16:43:25", "commits": 4 } ], "_score": 6.60552052343747, "_indexed": true, "_nocasepkg": "smccnet", "_universes": [ "kechrislab", "abhinavvpundirr" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.7", "date": "2026-05-16T09:32:41.000Z", "distro": "noble", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "560443d8890a432b74941b7f53168900cf8b90d7412bb80b8c75a44d21b622f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.6.0", "os": "linux", "version": "2.0.7", "date": "2026-05-16T09:33:20.000Z", "distro": "noble", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "e53e09c3c4eaf3f025c43892ee0f5cb0b8df6121af29564abc811035128c0841", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.5.3", "os": "mac", "version": "2.0.7", "date": "2026-05-16T09:32:21.000Z", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "3679f2bb29799a486e0b4a1bf77a829798a2dea6baa41cd83e202e584b4e29f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.6.0", "os": "mac", "version": "2.0.7", "date": "2026-05-16T09:32:29.000Z", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "9fb316fb7213fed860d143c4394c74af35afe85d987eccc75facfb5f90495ed8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.7.0", "os": "win", "version": "2.0.7", "date": "2026-05-16T09:31:14.000Z", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "74681937f06b31730ec0d3c2ca3c58227cc4695a47dc3bbcb378c50e73ff1bd0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.5.3", "os": "win", "version": "2.0.7", "date": "2026-05-16T09:31:14.000Z", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "fad70ef5fd8985bcab9ff46b064790578aac50f734d0815b9b94c12369f4e509", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.6.0", "os": "win", "version": "2.0.7", "date": "2026-05-16T09:31:28.000Z", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "54593c90a0c23b561d5f5fb9f16e38d70451cdfdecde7c95dbb4596a7cd9def7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" }, { "r": "4.6.0", "os": "wasm", "version": "2.0.7", "date": "2026-06-02T18:03:19.000Z", "commit": "b863af02091c2738d73fc96bd80891bf17d6261f", "fileid": "a1c52ec3001012da3b8b43cf775ce41d229ce97fbb4bbf3163a822a97e82a078", "status": "success", "buildurl": "https://github.com/r-universe/kechrislab/actions/runs/25958389617" } ] }