{ "_id": "6ac21cbe773a0037682c2335", "Package": "epiomics", "Title": "Analysis of Omics Data in Observational Studies", "Version": "1.2.0", "Authors@R": "person(\"Jesse\", \"Goodrich\", , \"jagoodri@usc.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6615-0472\"))", "Description": "A collection of fast and flexible functions for analyzing\nomics data in observational studies. Multiple different\napproaches for integrating multiple environmental/genetic\nfactors, omics data, and/or phenotype data are implemented.\nThis includes functions for performing omics wide association\nstudies with one or more variables of interest as the exposure\nor outcome; a function for performing a meet in the middle\nanalysis for linking exposures, omics, and outcomes (as\ndescribed by Chadeau-Hyam et al., (2010)\n); and a function for\nperforming a mixtures analysis across all omics features using\nquantile-based g-Computation (as described by Keil et al.,\n(2019) ).", "License": "GPL (>= 3)", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://goodrich-lab.r-universe.dev", "Date/Publication": "2025-02-14 04:44:14 UTC", "RemoteUrl": "https://github.com/goodrich-lab/epiomics", "RemoteRef": "HEAD", "RemoteSha": "d71ab603d52c589e011f097a719f81669be652ef", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-04 09:25:34 UTC", "User": "root" }, "Author": "Jesse Goodrich [aut, cre] (ORCID:\n)", "Maintainer": "Jesse Goodrich ", "_user": "goodrich-lab", "_type": "src", "_file": "epiomics_1.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/350bff6509ba7e2bef656523ee073c0486dd8ba7cd3873324fa7f425ab31db19", "_filesize": 457790, "_sha256": "350bff6509ba7e2bef656523ee073c0486dd8ba7cd3873324fa7f425ab31db19", "_expires": "2027-01-12T09:30:36.000Z", "_created": "2026-10-04T09:25:34.000Z", "_published": "2026-10-04T09:30:38.532Z", "_jobs": [ { "job": 111406354035, "time": 188, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11298974482" }, { "job": 111406354052, "time": 164, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11299382415" }, { "job": 111406354008, "time": 263, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11299567129" }, { "job": 111406354040, "time": 206, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11298889591" }, { "job": 111405824186, "time": 199, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11299342251" }, { "job": 111406354038, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11299835083" }, { "job": 111406354054, "time": 134, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11299139171" }, { "job": 111406354092, "time": 113, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11299562048" }, { "job": 111406354058, "time": 124, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11299209095" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738", "_status": "success", "_upstream": "https://github.com/goodrich-lab/epiomics", "_commit": { "id": "d71ab603d52c589e011f097a719f81669be652ef", "author": "Jesse Goodrich ", "committer": "Jesse Goodrich ", "message": "update dependencies\n", "time": 1739508254 }, "_maintainer": { "name": "Jesse Goodrich", "email": "jagoodri@usc.edu", "login": "jagoodrich", "orcid": "0000-0001-6615-0472", "description": "Assistant Professor at USC Department of Population and Public Health Sciences", "uuid": 32161948 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "qgcomp", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "goodrich-lab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "jagoodrich", "count": 76, "uuid": 32161948 } ], "_userbio": { "uuid": 128401716, "type": "organization", "name": "Goodrich Laboratory on Exposome And Precision Sciences at USC", "followers": 5 }, "_downloads": { "count": 384, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epiomics" }, "_devurl": "https://github.com/goodrich-lab/epiomics", "_searchresults": 12, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/epiomics.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/goodrich-lab/epiomics", "_realowner": "goodrich-lab", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2023-01-09" }, { "version": "1.0.0", "date": "2023-03-15" }, { "version": "1.1.0", "date": "2024-02-26" }, { "version": "1.2.0", "date": "2025-02-14" } ], "_exports": [ "coef_plot_from_owas", "meet_in_middle", "owas", "owas_clogit", "owas_qgcomp", "volcano_owas" ], "_datasets": [ { "name": "example_data", "title": "Example data with multiple exposures, multiple outcomes,", "object": "example_data", "class": [ "data.frame" ], "fields": [ "id", "id2", "sex", "age", "weight", "case_control_set", "cc_status", "exposure1", "exposure2", "exposure3", "exposure4", "disease1", "disease2", "diseasecat1", "diseasecat2", "diseasecat3", "feature_V1", "feature_V2", "feature_V3", "feature_V4", "feature_V5", "feature_V6", "feature_V7", "feature_V8", "feature_V9", "feature_V10", "feature_V11", "feature_V12", "feature_V13", "feature_V14", "feature_V15", "feature_V16", "feature_V17", "feature_V18", "feature_V19", "feature_V20", "feature_V21", "feature_V22", "feature_V23", "feature_V24", "feature_V25", "feature_V26", "feature_V27", "feature_V28", "feature_V29", "feature_V30", "feature_V31", "feature_V32", "feature_V33", "feature_V34", "feature_V35", "feature_V36", "feature_V37", "feature_V38", "feature_V39", "feature_V40", "feature_V41", "feature_V42", "feature_V43", "feature_V44", "feature_V45", "feature_V46", "feature_V47", "feature_V48", "feature_V49", "feature_V50", "feature_V51", "feature_V52", "feature_V53", "feature_V54", "feature_V55", "feature_V56", "feature_V57", "feature_V58", "feature_V59", "feature_V60", "feature_V61", "feature_V62", "feature_V63", "feature_V64", "feature_V65", "feature_V66", "feature_V67", "feature_V68", "feature_V69", "feature_V70", "feature_V71", "feature_V72", "feature_V73", "feature_V74", "feature_V75", "feature_V76", "feature_V77", "feature_V78", "feature_V79", "feature_V80", "feature_V81", "feature_V82", "feature_V83", "feature_V84", "feature_V85", "feature_V86", "feature_V87", "feature_V88", "feature_V89", "feature_V90", "feature_V91", "feature_V92", "feature_V93", "feature_V94", "feature_V95", "feature_V96", "feature_V97", "feature_V98", "feature_V99", "feature_V100" ], "rows": 400, "table": true, "tojson": true } ], "_help": [ { "page": "coef_plot_from_owas", "title": "Create volcano plot using results from owas", "topics": [ "coef_plot_from_owas" ] }, { "page": "example_data", "title": "Example data with multiple exposures, multiple outcomes,", "topics": [ "example_data" ] }, { "page": "meet_in_middle", "title": "Perform 'omics wide association study", "topics": [ "meet_in_middle" ] }, { "page": "owas", "title": "Perform 'omics wide association study", "topics": [ "owas" ] }, { "page": "owas_clogit", "title": "Perform 'omics wide association study for matched case control studies", "topics": [ "owas_clogit" ] }, { "page": "owas_qgcomp", "title": "Perform omics wide association study using qgcomp", "topics": [ "owas_qgcomp" ] }, { "page": "volcano_owas", "title": "Create volcano plot using results from owas", "topics": [ "volcano_owas" ] } ], "_readme": "https://github.com/goodrich-lab/epiomics/raw/HEAD/README.md", "_rundeps": [ "abind", "AER", "arm", "backports", "boot", "broom", "car", "carData", "cli", "coda", "codetools", "colorspace", "cowplot", "cpp11", "data.table", "Deriv", "digest", "doBy", "dplyr", "farver", "forecast", "Formula", "fracdiff", "future", "future.apply", "generics", "ggplot2", "ggrepel", "globals", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "listenv", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "parallelly", "pbkrtest", "pillar", "pkgconfig", "pscl", "purrr", "qgcomp", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rootSolve", "S7", "sandwich", "scales", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_score": 2.778151250383644, "_indexed": true, "_nocasepkg": "epiomics", "_universes": [ "goodrich-lab", "jagoodrich" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0", "date": "2026-10-04T09:28:19.000Z", "distro": "resolute", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/da74c08a4d38f48c70f529fe09b8d321f91b7f45b8be672e95db474f8740d996", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.6.1", "os": "linux", "version": "1.2.0", "date": "2026-10-04T09:27:41.000Z", "distro": "resolute", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/a58ed61a08cf47e3acb2d5d6bb7c0479de14c20b83091f8915f10bde810081e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0", "date": "2026-10-04T09:28:29.000Z", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/d2e7d261e745849d33ec25bb8b519ee737675b5fc0e9c1793257c1d209e4c840", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.6.1", "os": "mac", "version": "1.2.0", "date": "2026-10-04T09:27:57.000Z", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/392cc945e28d1fffcb27e4c6ed82ac09fa39a12a7574b45d951d5fee514147b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.0", "date": "2026-10-04T09:27:41.000Z", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/8431cc5cec25afdf470c7687573d0bc4d023f99092ab272911bc895a2ce7df03", "status": "success", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.7.0", "os": "win", "version": "1.2.0", "date": "2026-10-04T09:26:58.000Z", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/dc3b99ba6751b5db49f71aeee926cd4d88d6722b6750482c6d86a960ec3eda42", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.5.3", "os": "win", "version": "1.2.0", "date": "2026-10-04T09:26:45.000Z", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/fcc23a1af19e87bfe0f0509e80d7578b3c91f95993b0ab25d7df74c9900476aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" }, { "r": "4.6.1", "os": "win", "version": "1.2.0", "date": "2026-10-04T09:26:47.000Z", "commit": "d71ab603d52c589e011f097a719f81669be652ef", "fileid": "https://r2.ropensci.org/8baaf9d1593c1a8300af10e73b15c7f349820e39d43df929be5fc1def4481069", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/goodrich-lab/actions/runs/37191930738" } ] }