{ "_id": "6ad865f30d12c08e591b9a86", "Package": "iTOP", "Type": "Package", "Title": "Inferring the Topology of Omics Data", "Version": "1.0.2", "Author": "Nanne Aben", "Maintainer": "Nanne Aben ", "Description": "Infers a topology of relationships between different\ndatasets, such as multi-omics and phenotypic data recorded on\nthe same samples. We based this methodology on the RV\ncoefficient (Robert & Escoufier, 1976, ),\na measure of matrix correlation, which we have extended for\npartial matrix correlations and binary data (Aben et al., 2018,\n).", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "6.0.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-21 06:54:12 UTC", "User": "root" }, "Repository": "https://nanne-aben.r-universe.dev", "Date/Publication": "2018-06-13 08:16:06 UTC", "RemoteUrl": "https://github.com/cran/iTOP", "RemoteRef": "HEAD", "RemoteSha": "872aca22c8b9d7962f22c88df0fed832f005ef33", "_user": "nanne-aben", "_type": "src", "_file": "iTOP_1.0.2.tar.gz", "_fileid": "https://r2.ropensci.org/307fc7c30fa8e6527417d6ff465c71cc17bb6c384f51c17a0bacdada01b0d039", "_filesize": 248550, "_sha256": "307fc7c30fa8e6527417d6ff465c71cc17bb6c384f51c17a0bacdada01b0d039", "_expires": "2027-01-29T07:12:49.000Z", "_created": "2026-10-21T06:54:12.000Z", "_published": "2026-10-21T07:12:51.353Z", "_buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 119083444170, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12326104633" }, { "job": 119083443952, "time": 244, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12327285688" }, { "job": 119083443910, "time": 197, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12327168493" }, { "job": 119083444055, "time": 164, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12326759512" }, { "job": 119081395857, "time": 351, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12326228774" }, { "job": 119083444039, "time": 195, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12327335185" }, { "job": 119083443946, "time": 87, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12326542034" }, { "job": 119083444396, "time": 99, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12327180587" }, { "job": 119083443954, "time": 357, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12327455122" } ], "_upstream": "https://github.com/cran/iTOP", "_commit": { "id": "872aca22c8b9d7962f22c88df0fed832f005ef33", "author": "Nanne Aben ", "committer": "cran-robot ", "message": "version 1.0.2\n", "time": 1528877766 }, "_maintainer": { "name": "Nanne Aben", "email": "nanne.aben@gmail.com", "login": "nanne-aben", "description": "", "uuid": 47976799 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "Matrix", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "NMF", "role": "Suggests" }, { "package": "pcalg", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "nanne-aben", "count": 3, "uuid": 47976799 } ], "_userbio": { "uuid": 47976799, "type": "user", "name": "nanne-aben", "followers": 6 }, "_downloads": { "count": 426, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/iTOP" }, "_searchresults": 19, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/iTOP.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "nanne-aben", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2018-03-22" }, { "version": "1.0.1", "date": "2018-04-04" }, { "version": "1.0.2", "date": "2018-06-13" } ], "_exports": [ "compute.config.matrices", "compute.config.matrix", "inner.product", "intersect.samples", "jaccard", "process.custom.config.matrix", "run.bootstraps", "run.permutations", "rv.coef", "rv.conf.interval", "rv.cor.matrix", "rv.link.significance", "rv.pcor", "rv.pval" ], "_help": [ { "page": "bootstrap.config.matrices", "title": "Performing a single bootstrap", "topics": [ "bootstrap.config.matrices" ] }, { "page": "compute.config.matrices", "title": "Compute configuration matrices", "topics": [ "compute.config.matrices" ] }, { "page": "compute.config.matrix", "title": "Computes a configuration matrix", "topics": [ "compute.config.matrix" ] }, { "page": "inner.product", "title": "Inner product similarity.", "topics": [ "inner.product" ] }, { "page": "intersect.samples", "title": "Intersect samples between datasets.", "topics": [ "intersect.samples" ] }, { "page": "jaccard", "title": "Jaccard similarity.", "topics": [ "jaccard" ] }, { "page": "permute.config.matrices", "title": "Performing a permutation", "topics": [ "permute.config.matrices" ] }, { "page": "process.custom.config.matrix", "title": "Process a custom configuration matrix.", "topics": [ "process.custom.config.matrix" ] }, { "page": "run.bootstraps", "title": "Bootstrapping procedure", "topics": [ "run.bootstraps" ] }, { "page": "run.permutations", "title": "Permutations for significance testing", "topics": [ "run.permutations" ] }, { "page": "rv.coef", "title": "Computes the RV coefficient", "topics": [ "rv.coef" ] }, { "page": "rv.conf.interval", "title": "Determining a confidence interval for the (partial) RV coefficient", "topics": [ "rv.conf.interval" ] }, { "page": "rv.cor.matrix", "title": "A correlation matrix of RV coefficients", "topics": [ "rv.cor.matrix" ] }, { "page": "rv.link.significance", "title": "Wrapper function to determine significance in the PC algorithm", "topics": [ "rv.link.significance" ] }, { "page": "rv.pcor", "title": "Determining a (partial) RV coefficient", "topics": [ "rv.pcor" ] }, { "page": "rv.pval", "title": "Determining a p-value the (partial) RV coefficient", "topics": [ "rv.pval" ] } ], "_rundeps": [ "corpcor", "lattice", "Matrix" ], "_vignettes": [ { "source": "vignette.Rmd", "filename": "vignette.html", "title": "A quick introduction to iTOP", "author": "Nanne Aben", "engine": "knitr::rmarkdown", "headings": [ "Inferring a topology using continuous value datasets", "Artificial data", "Matrix correlations", "Statistical inference for matrix correlations", "Statistical inference for partial matrix correlations", "Inferring a topology of interactions between datasets", "Inferring a topology using data type specific configuration matrices", "Computing data type specific configuration matrices", "Using the data type specific configuration matrices" ], "created": "2018-03-22 11:04:54", "modified": "2018-06-13 08:16:06", "commits": 3 } ], "_score": 2.278753600952829, "_indexed": true, "_nocasepkg": "itop", "_universes": [ "nanne-aben" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-10-21T06:56:25.000Z", "distro": "resolute", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/12471487db4cca43439d527be48b85911b6d913115588b08bbee0e3130926e11", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.6.1", "os": "linux", "version": "1.0.2", "date": "2026-10-21T06:58:13.000Z", "distro": "resolute", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/d981e66d524b0ebed93dd2313ee73cedde552719b61868a79c770cbb724f216d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-10-21T07:09:40.000Z", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/95574e5afd14ac6ab4636cd09d370d3d958ae8815c4563d60867c69a264ebc06", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.6.1", "os": "mac", "version": "1.0.2", "date": "2026-10-21T07:11:37.000Z", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/5f604f9ae46eda050e26278aed272209757fd920288f6ac127410624075db244", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-10-21T06:57:42.000Z", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/eeda3e3c80835627dfe248ccc5d4598dfd9ec4c5d03dba67c375181eae116577", "status": "success", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.7.0", "os": "win", "version": "1.0.2", "date": "2026-10-21T06:55:35.000Z", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/e3abd4d24a4834b07cf0f70848fd77efadaf5226c93230777c019cc0aec85b3b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.5.3", "os": "win", "version": "1.0.2", "date": "2026-10-21T06:55:42.000Z", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/29e9e0a985e420aaa6b219a23b436e948e1225bb910b741e542efb8472f32b38", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" }, { "r": "4.6.1", "os": "win", "version": "1.0.2", "date": "2026-10-21T06:59:58.000Z", "commit": "872aca22c8b9d7962f22c88df0fed832f005ef33", "fileid": "https://r2.ropensci.org/e6b1884c65c4ab7f7e96d1e09eca288111d5db0e21b4635feffa1321a8e9a57e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nanne-aben/actions/runs/39557707882" } ] }