{ "_id": "6a1ff4a9b401979e73442ec8", "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": "2025-10-06 18:06:45 UTC", "RemoteUrl": "https://github.com/tgbrooks/dependentsimr", "RemoteRef": "HEAD", "RemoteSha": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 09:26:49 UTC", "User": "root" }, "Author": "Thomas Brooks [aut, cre, cph] (ORCID:\n)", "Maintainer": "Thomas Brooks ", "MD5sum": "dc52e7a1ad9f29428746c2ad117e18f1", "_user": "tgbrooks", "_type": "src", "_file": "dependentsimr_1.0.0.0.tar.gz", "_fileid": "2a3311b58f43621e2cc9e20b07dd9681a5a3995c384c9f5e1262ac6eb25fdbcd", "_filesize": 194425, "_sha256": "2a3311b58f43621e2cc9e20b07dd9681a5a3995c384c9f5e1262ac6eb25fdbcd", "_created": "2026-06-03T09:26:49.000Z", "_published": "2026-06-03T09:32:25.717Z", "_distro": "noble", "_jobs": [ { "job": 79262975245, "time": 308, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7380812383" }, { "job": 79262975204, "time": 192, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7380769549" }, { "job": 79262975258, "time": 203, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7380762155" }, { "job": 79262975269, "time": 141, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7380740039" }, { "job": 79262285875, "time": 236, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7380696946" }, { "job": 79262975225, "time": 172, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7380762204" }, { "job": 79262975443, "time": 103, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7380736591" }, { "job": 79262975361, "time": 110, "config": 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}, { "package": "S4Vectors", "version": ">= 0.44.0", "role": "Suggests" }, { "package": "SummarizedExperiment", "version": ">= 1.36.0", "role": "Suggests" }, { "package": "MASS", "version": ">= 7.3", "role": "Suggests" }, { "package": "corpcor", "version": ">= 1.6.0", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "Matrix", "version": ">= 1.7", "role": "Suggests" }, { "package": "sparsesvd", "version": ">= 0.2", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.50", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "remotes", "role": "Suggests" }, { "package": "tidyverse", "version": ">= 2.0.0", "role": "Suggests" } ], "_owner": "tgbrooks", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 2 }, { "week": "2025-27", "n": 8 }, { "week": "2025-28", "n": 5 }, { "week": "2025-32", "n": 1 }, { "week": "2025-41", "n": 1 } ], "_tags": [], "_stars": 2, "_contributors": [ { "user": "tgbrooks", "count": 82, "uuid": 1789527 } ], "_userbio": { "uuid": 1789527, "type": "user", "name": "Thomas Brooks", "description": "Bioinformatician at UPenn ITMAT Bioinformatics Lab" }, "_downloads": { "count": 112, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dependentsimr" }, "_devurl": "https://github.com/tgbrooks/dependentsimr", "_searchresults": 12, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dependentsimr.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": 4.778151250383644, "_indexed": true, "_nocasepkg": "dependentsimr", "_universes": [ "tgbrooks" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0.0", "date": "2026-06-03T09:31:46.000Z", "distro": "noble", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "df87cb2fe1eb3fa814d2e7f21cdda02d2222f811ede3fbee28430df0ede5af8c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0.0", "date": "2026-06-03T09:29:47.000Z", "distro": "noble", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "e3caeaae8c89a7dde2fd9fd2b9aeba95118a5d24c05c61175d66bd519923dfaf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0.0", "date": "2026-06-03T09:29:33.000Z", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "65241a4bb6b776999fe822d2a7e948783e787f1d023f3ae504810ed813b110e5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0.0", "date": "2026-06-03T09:28:37.000Z", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "bf6eccea954c96f93adef20ae4de0db33ae433398e141a841f8dba2ee7bea91e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0.0", "date": "2026-06-03T09:29:54.000Z", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "511cf0f8d6e85a14ee594ace5bdc1963347b9d5ae25206a10375d033642e4663", "status": "success", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.7.0", "os": "win", "version": "1.0.0.0", "date": "2026-06-03T09:28:17.000Z", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "8bcb2804371410006c625212e4325ee54882396452d34d7fd7302952470761c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.5.3", "os": "win", "version": "1.0.0.0", "date": "2026-06-03T09:28:24.000Z", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "f8ec168b07d2752bb60d60e71213ea5cb02e99508cc4503324fee6bf3465f978", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" }, { "r": "4.6.0", "os": "win", "version": "1.0.0.0", "date": "2026-06-03T09:29:25.000Z", "commit": "1af2c556bff0e51722e5c0a52117df2dd4bb4000", "fileid": "bf62f1fa2456cdcc87c111224fb6f9e6fa02c1d3f12b6bbf3e103ac78ac1816e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tgbrooks/actions/runs/26875696304" } ] }