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Package also enables estimating of\nco-occurrence of diseases across the network and specific\nclusters pointing towards shared/common mechanisms.", "License": "Artistic-2.0", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "RdMacros": "Rdpack", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "BugReports": "https://github.com/lptolik/BioNAR/issues/", "biocViews": "Software, GraphAndNetwork, Network", "LazyData": "true", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-29 11:47:06 UTC", "RemoteUrl": "https://github.com/bioc/BioNAR", "RemoteRef": "HEAD", "RemoteSha": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-14 09:42:58 UTC", "User": "root" }, "Author": "Colin Mclean [aut],\nAnatoly Sorokin [aut, cre],\nOksana Sorokina [aut],\nJ. Douglas Armstrong [aut, fnd],\nT. 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annotation.", "topics": [ "escapeAnnotation" ] }, { "page": "evalCentralitySignificance", "title": "Compare distance distributions of internal and external distances", "topics": [ "evalCentralitySignificance" ] }, { "page": "findLCC", "title": "Find Largest Connected Component of the graph", "topics": [ "findLCC" ] }, { "page": "FitDegree", "title": "Fit Power Law to degree distribution.", "topics": [ "fitDegree" ] }, { "page": "fitSigmoid", "title": "Fit Fold-enrichment distribution to sigmoid function", "topics": [ "fitSigmoid" ] }, { "page": "flatfile_human_gene2HDO.csv", "title": "Human Gene Disease Associations (GDA)", "topics": [ "flatfile_human_gene2HDO.csv" ] }, { "page": "flatfile.go.BP.csv", "title": "Annotation from Gene Ontology Biological Process (GO_BP)", "topics": [ "flatfile.go.BP.csv" ] }, { "page": "flatfile.go.CC.csv", "title": "Annotation from Gene Ontology Cellular Compartment (GO_CC)", "topics": [ "flatfile.go.CC.csv" ] }, { "page": "flatfile.go.MF.csv", "title": 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It fails if any duplicate found.", "topics": [ "getIDs" ] }, { "page": "getPA", "title": "Generate random graph from reference", "topics": [ "getPA" ] }, { "page": "getRandomGraphCentrality", "title": "Centrality measures for random graphs induced by input one", "topics": [ "getRandomGraphCentrality" ] }, { "page": "getRobustness", "title": "Calculate cluster robustness from consensus matrix", "concept": [ "Robustness Functions" ], "topics": [ "getRobustness" ] }, { "page": "gofs", "title": "Goodnes of fit KS test", "topics": [ "gofs" ] }, { "page": "law-class", "title": "Result of PawerLaw fit", "topics": [ "law-class" ] }, { "page": "layoutByCluster", "title": "Calculate layout based upon membership", "topics": [ "layoutByCluster" ] }, { "page": "layoutByRecluster", "title": "Calculate two-level layout from recluster matrix", "topics": [ "layoutByRecluster" ] }, { "page": "makeConsensusMatrix", "title": "Function to make random resampling consensus matrix in memory", "concept": [ "Robustness Functions" ], "topics": [ "makeConsensusMatrix" ] }, { "page": "makeMembership", "title": "Create membership 'data.frame' from graph for arbitrary annotation", "topics": [ "makeMembership" ] }, { "page": "markBowTie", "title": "Calculates bow-tie decomposition and marks vertices with one of the following in the 'BowTie' attribute: • SCC - maximal strong connected component; • IN - vertices not in SCC, but SCC is reachable from them; • OUT - vertices not in SCC, but reachable from SCC; • TU - vertices not in all three above, but reachable from IN and OUT is reachable from them (TUBES); • IDR - vertices not in SCC, but they are reachable from IN and OUT is NOT reachable from them (INTENDRILS); • ODR - vertices not is SCC, but they are NOT reachable from IN and OUT is reachable from them (OUTTENDRILS); • OTR - all other vertices.", "topics": [ "markBowTie" ] }, { "page": "metlMatrix", "title": "Convert sparce matrix into triplet 'data.frame'.", "topics": [ "metlMatrix" ] }, { "page": "normModularity", "title": "Calculates the normalised network modularity value.", "topics": [ "normModularity" ] }, { "page": "permute", "title": "Randomly shuffle annotations", "topics": [ "permute" ] }, { "page": "plotBridgeness", "title": "Plot Bridgeness values", "topics": [ "plotBridgeness" ] }, { "page": "plotEntropy", "title": "Plot graph entropy values versus vertex degree for each perturbed vertex value.", "concept": [ "Entropy Functions" ], "topics": [ "plotEntropy" ] }, { "page": "plotRatio", "title": "Plot fraction of enriched communities", "topics": [ "plotRatio" ] }, { "page": "plotSigmoid", "title": "Plot results of the sigmoid fit", "topics": [ "plotSigmoid" ] }, { "page": "PPI_Presynaptic.csv", "title": "Table of protein protein interactions for presynaptic compartment", "topics": [ "PPI_Presynaptic.csv" ] }, { "page": "PPI_Presynaptic.gml", "title": "PPI graph for presynaptic compartment", "topics": [ "PPI_Presynaptic.gml" ] }, { "page": "prepareGDA", "title": "Function to return vertex annotation from a graph in the Vertex Annotation form and format it for further analysis.", "topics": [ "prepareGDA" ] }, { "page": "PresynAn.csv", "title": "Presynaptic genes specific functional annotation", "topics": [ "PresynAn.csv" ] }, { "page": "recluster", "title": "Hierarchical graph clustering", "topics": [ "recluster" ] }, { "page": "removeVertexTerm", "title": "Remove vertex property.", "topics": [ "removeVertexTerm" ] }, { "page": "runPermDisease", "title": "Calculate disease-disease pair overlaps on permuted network to estimate its statistical significance", "topics": [ "runPermDisease" ] }, { "page": "sampleDegBinnedGDA", "title": "Function to randomly shuffle vertex annotation terms, whilst preserving the vertex degree originally found with that annotation term..", "topics": [ "sampleDegBinnedGDA" ] }, { "page": "sampleGraphClust", "title": "Perturbe graph and calculate its clustering", "topics": [ "sampleGraphClust" ] }, { "page": "SCH_flatfile.csv", "title": "Schizopherina related synaptic gene functional annotation.", "topics": [ "SCH_flatfile.csv" ] }, { "page": "summaryStats", "title": "Calculate summary statistics from enrichment table", "topics": [ "summaryStats" ] }, { "page": "unescapeAnnotation", "title": "Unescape annotation strings", "topics": [ "unescapeAnnotation" ] }, { "page": "zeroNA", "title": "Auxiliary function to replace NAs with zeros.", "topics": [ "zeroNA" ] } ], "_readme": "https://github.com/bioc/BioNAR/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "checkmate", "cli", "cluster", "codetools", "colorspace", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "digest", "doParallel", "dplyr", "dynamicTreeCut", "evaluate", "farver", "fastcluster", "fastmap", "fastmatch", "fgsea", "fontawesome", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "ggplot2", "ggrepel", "glue", "GO.db", "graph", "gridExtra", "gtable", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "latex2exp", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "memoise", "mime", "minpack.lm", "nnet", "openssl", "org.Hs.eg.db", "pillar", "pkgconfig", "png", "poweRlaw", "pracma", "preprocessCore", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "rlang", "rmarkdown", "rpart", "RSpectra", "rSpectral", "RSQLite", "rstudioapi", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "stringi", "stringr", "survival", "sys", "tibble", "tidyselect", "tinytex", "utf8", "vctrs", "viridis", "viridisLite", "WGCNA", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "BioNAR_overview.Rmd", "filename": "BioNAR_overview.html", "title": "BioNAR: Biological Network Analysis in R", "author": "Colin Mclean, Anatoly Sorokin, T. I. Simpson, J. Douglas Armstrong, Oksana Sorokina", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview of capabilities", "Build the network", "Build a network from a given data frame", "Use a predifined network", "Annotate the nodes with node attributes", "Gene name", "Diseases", "Schizopherina related synaptic gene functional annotation.", "Presynaptic functional annotation", "Functional annotation with Gene Ontology (GO)", "Estimate vertex centrality measures", "Estimate centrality measures with values added as vertex attributes.", "Get vertex centralities as a matrix.", "Get the centrality measures for random graph", "Power law fit", "Get entropy rate", "Get modularity. Normalised modularity.", "Clustering", "Reclustering", "Consensus matrix", "Cluster robustness", "Bridgeness", "Bridgeness plot", "Disease/annotation pairs", "Cluster overrepresentation", "Session Info" ], "created": "2022-10-21 06:01:46", "modified": "2025-02-26 01:23:33", "commits": 13 } ], "_score": 5.221414237842339, "_indexed": true, "_nocasepkg": "bionar", "_universes": [ "bioc", "lptolik" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-05-14T09:47:46.000Z", "distro": "noble", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "d4b00aeecdfa3e534082ecdf0d666c65cb7a206a0038e3a2322bdf69a540af30", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.6.0", "os": "linux", "version": "1.15.0", "date": "2026-05-14T09:48:10.000Z", "distro": "noble", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "8b5a4a80f86aaeff219453bf381d1873558b72ec48d4120d7f53110a196c911b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-05-14T09:45:18.000Z", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "6641b2e25595f6469b871113bb48fa90b75411435174537d10934517109ce59b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.6.0", "os": "mac", "version": "1.15.0", "date": "2026-05-14T09:46:05.000Z", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "f01bb5c838294a5a491c2af675c8656690a478f004d88de1fc93fe701625fb36", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-05-14T09:47:16.000Z", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "06d7d5acd7e92f5a154fadea1a369ab0537bff2dc88a948ec26bda723a643fdc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-05-14T09:45:46.000Z", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "fdbfb7f6919ad885e2a655e71ed285471888ff3df28ddbcfb474ff2bd9d9de62", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.6.0", "os": "win", "version": "1.15.0", "date": "2026-05-14T09:45:31.000Z", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "43e1a35dd1a3fe06284bbe796dde38932b572abad8235f666187f091e7c63b8e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-05-22T08:59:02.000Z", "commit": "5acd4d1e61c1fd9129eca169c68fdd6097b60a72", "fileid": "3a8c0af4f8f203021a632446f71687d66c621c3cb8db4cdc326f09fa870741cf", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25852923061" } ] }