{ "_id": "6a15719bacfb0bcc41d652c7", "Package": "graphsim", "Type": "Package", "Title": "Simulate Expression Data from 'igraph' Networks", "Version": "1.0.4", "Date": "2025-05-02", "Authors@R": "c(person(\"S. Thomas\", \"Kelly\",email = \"tomkellygenetics@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Michael A.\", \"Black\", email = \"mik.black@otago.ac.nz\", role = c(\"aut\", \"ths\")),\nperson(\"Robrecht\", \"Cannoodt\", role = c(\"ctb\")),\nperson(\"Jason Cory\", \"Brunson\", role = c(\"ctb\")))", "Description": "Functions to develop simulated continuous data (e.g., gene\nexpression) from a sigma covariance matrix derived from a graph\nstructure in 'igraph' objects. Intended to extend 'mvtnorm' to\ntake 'igraph' structures rather than sigma matrices as input.\nThis allows the use of simulated data that correctly accounts\nfor pathway relationships and correlations. This allows the use\nof simulated data that correctly accounts for pathway\nrelationships and correlations. Here we present a versatile\nstatistical framework to simulate correlated gene expression\ndata from biological pathways, by sampling from a multivariate\nnormal distribution derived from a graph structure. This\npackage allows the simulation of biological pathways from a\ngraph structure based on a statistical model of gene\nexpression. For example methods to infer biological pathways\nand gene regulatory networks from gene expression data can be\ntested on simulated datasets using this framework. This also\nallows for pathway structures to be considered as a confounding\nvariable when simulating gene expression data to test the\nperformance of genomic analyses.", "License": "GPL-3", "URL": "https://github.com/TomKellyGenetics/graphsim/", "BugReports": "https://github.com/TomKellyGenetics/graphsim/issues/", "LazyData": "TRUE", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "VignetteBuilder": "R.rsp", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 10:07:01 UTC", "User": "root" }, "Author": "S. Thomas Kelly [aut, cre], Michael A. Black [aut, ths],\nRobrecht Cannoodt [ctb], Jason Cory Brunson [ctb]", "Maintainer": "S. Thomas Kelly ", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://tomkellygenetics.r-universe.dev", "Date/Publication": "2025-05-12 21:44:29 UTC", "RemoteUrl": "https://github.com/tomkellygenetics/graphsim", "RemoteRef": "HEAD", "RemoteSha": "cb201c75c8f9c56bd3f3250ddd5afc2174de3fff", "MD5sum": "50b3f90fb2703f50b1cd871e334dc294", "_user": "tomkellygenetics", "_type": "src", "_file": "graphsim_1.0.4.tar.gz", "_fileid": "b8976d73a1ae4c285af15d715df1aab543ae2911b2896c96ce301e6b98cff4ed", "_filesize": 372351, "_sha256": "b8976d73a1ae4c285af15d715df1aab543ae2911b2896c96ce301e6b98cff4ed", "_created": "2026-05-26T10:07:01.000Z", "_published": "2026-05-26T10:10:35.019Z", "_distro": "noble", "_jobs": [ { "job": 77852154750, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7214356914" }, { "job": 77852154703, "time": 168, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7214357620" }, { "job": 77852154718, "time": 87, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7214331833" }, { "job": 77852154842, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7214337724" }, { "job": 77851629294, "time": 196, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7214301820" }, { "job": 77852154814, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7214346333" }, { "job": 77852155000, "time": 113, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7214339994" }, { "job": 77852154951, "time": 97, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7214334869" }, { "job": 77852154784, "time": 102, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7214336672" } ], "_buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26445767846", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/tomkellygenetics/graphsim", "_commit": { "id": "cb201c75c8f9c56bd3f3250ddd5afc2174de3fff", "author": "S. Thomas Kelly ", "committer": "S. Thomas Kelly ", "message": "update to pass cran checks\n", "time": 1747086269 }, "_maintainer": { "name": "S. Thomas Kelly", "email": "tomkellygenetics@gmail.com", "login": "tomkellygenetics", "linkedin": "in/tom-kelly-genetics", "twitter": "@tomkxy", "description": "Bioinformatician. Alumni @mikblacklab Otago, @minoda-lab RIKEN & @hugp-ri. The @carpentries instructor.\n\nGenomics | Health | Math | Stats | AWS Dev", "uuid": 5493325 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "gplots", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "matrixcalc", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "devtools", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.5", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "R.rsp", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" } ], "_owner": "tomkellygenetics", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "benchmarking", "gene-expression", "gene-regulatory-networks", "genetics", "genomic-data-analysis", "genomics", "graph-algorithms", "igraph-networks", "joss", "ngs-analysis", "simulated-data", "simulation-modeling" ], "_stars": 25, "_contributors": [ { "user": "tomkellygenetics", "count": 417, "uuid": 5493325 }, { "user": "rcannood", "count": 2, "uuid": 553642 } ], "_userbio": { "uuid": 5493325, "type": "user", "name": "Tom Kelly", "description": "Bioinformatician. 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