{ "_id": "6adb79cb58000136b5c82c0e", "Package": "dependentsimr", "Title": "Simulate Omics-Scale Data with Dependency", "Version": "1.0.0.0", "Authors@R": "person(\"Thomas\", \"Brooks\", , \"tgbrooks@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-6980-0079\"))", "Description": "Using a Gaussian copula approach, this package generates\nsimulated data mimicking a target real dataset. It supports\nnormal, Poisson, empirical, and 'DESeq2' (negative binomial\nwith size factors) marginal distributions. It uses an low-rank\nplus diagonal covariance matrix to efficiently generate\nomics-scale data. Methods are described in: Yang, Grant, and\nBrooks (2025) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "LazyData": "true", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Repository": "https://tgbrooks.r-universe.dev", "Date/Publication": "2026-10-23 14:13:03 UTC", "RemoteUrl": "https://github.com/tgbrooks/dependentsimr", "RemoteRef": "HEAD", "RemoteSha": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-23 14:55:43 UTC", "User": "root" }, "Author": "Thomas Brooks [aut, cre, cph] (ORCID:\n)", "Maintainer": "Thomas Brooks ", "_user": "tgbrooks", "_type": "src", "_file": "dependentsimr_1.0.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/4701dd1a104a7277d68330494202f6b72609aefda3a3df88cd2bf3b8179e22d8", "_filesize": 195411, "_sha256": "4701dd1a104a7277d68330494202f6b72609aefda3a3df88cd2bf3b8179e22d8", "_expires": "2027-01-31T15:14:17.000Z", "_created": "2026-10-23T14:55:43.000Z", "_published": "2026-10-23T15:14:19.168Z", "_upstream": "https://github.com/tgbrooks/dependentsimr", "_status": "success", "_maintainer": { "name": "Thomas Brooks", "email": "tgbrooks@gmail.com", "login": "tgbrooks", "orcid": "0000-0002-6980-0079", "description": "Bioinformatician at UPenn ITMAT Bioinformatics Lab", "uuid": 1789527 }, "_jobs": [ { "job": 120483252300, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12511055358" }, { "job": 120483252233, "time": 359, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12510861615" }, { "job": 120483252265, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12510444029" }, { "job": 120483252246, "time": 145, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12511590989" }, { "job": 120479818587, "time": 411, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12510472807" 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"tgbrooks", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-43", "n": 1 } ], "_tags": [ { "name": "v1.1", "date": "2026-10-23" } ], "_stars": 2, "_contributors": [ { "user": "tgbrooks", "count": 83, "uuid": 1789527 } ], "_userbio": { "uuid": 1789527, "type": "user", "name": "Thomas Brooks", "followers": 4, "description": "Bioinformatician at UPenn ITMAT Bioinformatics Lab" }, "_downloads": { "count": 248, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dependentsimr" }, "_devurl": "https://github.com/tgbrooks/dependentsimr", "_searchresults": 12, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dependentsimr.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/tgbrooks/dependentsimr", "_realowner": "tgbrooks", "_cranurl": true, "_releases": [ { "version": "1.0.0.0", "date": "2025-07-23" } ], "_exports": [ "draw_from_multivariate_corr", "get_random_structure", "match_with_spiked_wishart", "multi_sample_spiked_wishart", "remove_dependence", "sample_spiked_wishart", "sample_spiked_wishart_and_jac" ], "_datasets": [ { "name": "read_counts", "title": "GSE151923: cortex from 6-month-old wildtype C57BL/6 mice", "object": "read_counts", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "gene_id", "Arpp19_10_3", "Arpp19_4_1", "Arpp19_5_1", "Arpp19_5_3", "Arpp19_5_4", "Arpp19_6_1", "Arpp19_7_2", "Arpp19_9_1", "Dach1_11_1", "Dach1_2_2", "Dach1_3_1", "Dach1_5_3" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "draw_from_multivariate_corr", "title": "Draw random samples from the given random structure", "topics": [ "draw_from_multivariate_corr" ] }, { "page": "get_random_structure", "title": "Compute structure of dependency from a given data", "topics": [ "get_random_structure" ] }, { "page": "match_with_spiked_wishart", "title": "Compute what spiked SD values will give you the desired top eigenvalues by iteratively solving", "topics": [ "match_with_spiked_wishart" ] }, { "page": "multi_sample_spiked_wishart", "title": "Compute means of each singular value and the mean Jacobian, see sample_spiked_wishart_and_jac", "topics": [ "multi_sample_spiked_wishart" ] }, { "page": "read_counts", "title": "GSE151923: cortex from 6-month-old wildtype C57BL/6 mice", "topics": [ "read_counts" ] }, { "page": "remove_dependence", "title": "Remove all dependence in a random structure", "topics": [ "remove_dependence" ] }, { "page": "sample_spiked_wishart", "title": "Efficiently sample the singular values corresponding to a random Wishart matrix with spiked eigenvalues Specifically, if W = G G^T with each column of G drawn iid from N(0, Sigma), then W is a Wishart matrix and this function samples the singular values of G. The eigenvalues of W are just the squares of the singular values. Here, Sigma is diagonal with its leading entries from spiked_sd^2 and all remaining entries are population_sd^2.", "topics": [ "sample_spiked_wishart" ] }, { "page": "sample_spiked_wishart_and_jac", "title": "Efficiently sample the singular values corresponding to a random Wishart matrix with spiked eigenvalues and the Jacobian I.e., these are the singular values of G if GG^T is Wishart. The square of these give the eigenvalues of the random Wishart matrix.", "topics": [ "sample_spiked_wishart_and_jac" ] } ], "_readme": "https://github.com/tgbrooks/dependentsimr/raw/HEAD/README.md", "_rundeps": [ "rlang" ], "_vignettes": [ { "source": "simulate_data.Rmd", "filename": "simulate_data.html", "title": "Simulating data with dependentsimr", "engine": "knitr::rmarkdown", "headings": [ "Setup", "Load data", "Get Dependence Structure", "Generate Data", "Simulate Control Data", "Simulate Differentially Expressed Data", "Plot the generated data" ], "created": "2025-01-28 14:31:13", "modified": "2025-07-11 17:25:47", "commits": 2 } ], "_score": 4.079181246047625, "_indexed": true, "_nocasepkg": "dependentsimr", "_universes": [ "tgbrooks" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0.0", "date": "2026-10-23T14:58:34.000Z", "distro": "resolute", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/e69b2b5a4db2aae8e1fdbe39e3dcf6371080ea9fbd38e6f1585770b69448ecf2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0.0", "date": "2026-10-23T15:01:25.000Z", "distro": "resolute", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/4f6f446b7301ce781f3f4b0ed8074f1e9038d4a5c30a0d1c040a0563ca605e22", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0.0", "date": "2026-10-23T15:13:04.000Z", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/0d390d3979dae0cff831e3f0d5760d12880884035424ccd8fc5810acffa6b08f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0.0", "date": "2026-10-23T15:08:51.000Z", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/196c85d261de16a07077ec1c3900532d553c499bc42ddb2d3da414cdbace09cd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0.0", "date": "2026-10-23T15:00:42.000Z", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/7b41a2a1177e325c49a5abb23c40e8ccbba59f071ba7d752640a835f8d7765ba", "status": "success", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.7.0", "os": "win", "version": "1.0.0.0", "date": "2026-10-23T14:57:03.000Z", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/2a155574e2470fd50faf36bc837356e31d78f4a87553761937465dd904b054b1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.5.3", "os": "win", "version": "1.0.0.0", "date": "2026-10-23T14:57:19.000Z", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/cd8d36dde7c56045d3d211c862ff679d57be137ef3dcf35d2ffd744605eccef4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" }, { "r": "4.6.1", "os": "win", "version": "1.0.0.0", "date": "2026-10-23T15:01:02.000Z", "commit": "5c6ef0af4792ff62a28e0e78ec5ededc1ed6783a", "fileid": "https://r2.ropensci.org/3e577227cb50a0acea47fa6d742b17781e3fdeb73f5da4266699ff743896647f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/39972824984" } ] }