{ "_id": "6af4bbc9535793c853328cf0", "Package": "depower", "Title": "Power Analysis for Differential Expression Studies", "Version": "2026.11.11", "Authors@R": "c(\nperson(\ngiven = \"Brett\",\nfamily = \"Klamer\",\nemail = \"code@brettklamer.com\",\ncomment = c(ORCID = \"0000-0002-8334-4831\"),\nrole = c(\"aut\", \"cre\")\n),\nperson(\ngiven = \"Lianbo\",\nfamily = \"Yu\",\nemail = \"lianbo.yu@osumc.edu\",\ncomment = c(ORCID = \"0000-0002-2025-2585\"),\nrole = c(\"aut\")\n)\n)", "Description": "Provides a convenient framework to simulate data, run\nhypothesis tests, estimate power, and plot the results for\ndifferential expression studies. The simulation-based framework\nis described in Klamer and Yu (2026)\n. Outcomes may be lognormal,\nnegative binomial, or bivariate negative binomial. Supported\ndesigns are one-sample, independent two-sample, and dependent\ntwo-sample comparisons. Built-in tests include t-tests, Wald\ntests, and likelihood ratio tests. User-defined tests are also\naccepted. The significance level can be set to control the\nper-family error rate or the family-wise error rate. Negative\nbinomial methods are described in Yu, Fernandez, and Brock\n(2017) and Yu, Fernandez, and\nBrock (2020) .", "URL": "https://brettklamer.com/work/depower/,\nhttps://bitbucket.org/bklamer/depower/", "License": "MIT + file LICENSE", "RdMacros": "Rdpack", "Language": "en-US", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://bklamer.r-universe.dev", "Date/Publication": "2026-11-11 18:05:19 UTC", "RemoteUrl": "https://bitbucket.org/bklamer/depower", "RemoteRef": "HEAD", "RemoteSha": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-11 18:55:41 UTC", "User": "root" }, "Author": "Brett Klamer [aut, cre] (ORCID:\n),\nLianbo Yu [aut] (ORCID: )", "Maintainer": "Brett Klamer ", "_user": "bklamer", "_type": "src", "_file": "depower_2026.11.11.tar.gz", "_fileid": "https://r2.ropensci.org/ce0987521e1cc84527927bac2887d709ece5308af4e5faaee4ba637c266ae7fc", "_filesize": 1176185, "_sha256": "ce0987521e1cc84527927bac2887d709ece5308af4e5faaee4ba637c266ae7fc", "_expires": "2027-02-19T19:02:31.000Z", "_created": "2026-11-11T18:55:41.000Z", "_published": "2026-11-11T19:02:33.253Z", "_upstream": "https://bitbucket.org/bklamer/depower", "_status": "success", "_maintainer": { "name": "Brett Klamer", "email": "code@brettklamer.com", "login": "bklamer", "orcid": "0000-0002-8334-4831", "description": "I don't use github for personal projects.", "uuid": 8397446 }, "_jobs": [ { "job": 130738171622, "time": 253, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13883839518" }, { "job": 130738171569, "time": 192, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13884623506" }, { "job": 130738171718, "time": 174, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13885272235" }, { "job": 130738171623, "time": 192, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13884463510" }, { "job": 130735961172, "time": 246, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13884697714" }, { "job": 130738171584, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13885606133" }, { "job": 130738171744, "time": 358, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13885282529" }, { "job": 130738171647, "time": 273, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13885651513" }, { "job": 130738171634, "time": 325, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13884824621" } ], "_buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069", "_commit": { "id": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "author": "Brett Klamer ", "committer": "Brett Klamer ", "message": "Release 2026.11.11\n", "time": 1794420319 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Rdpack", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "mvnfast", "role": "Imports" }, { "package": "glmmTMB", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "multidplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "tinytest", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bitbucket-bklamer", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 6 }, { "week": "2026-05", "n": 9 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 1 }, { "week": "2026-25", "n": 1 }, { "week": "2026-45", "n": 9 }, { "week": "2026-46", "n": 3 } ], "_tags": [], "_userbio": { "uuid": 8397446, "type": "user", "name": "Brett Klamer", "followers": 4, "description": "I don't use github for personal projects." }, "_downloads": { "count": 322, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/depower" }, "_devurl": "https://bitbucket.org/bklamer/depower", "_searchresults": 63, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/depower.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://bitbucket.org/bklamer/depower", "_realowner": "bklamer", "_cranurl": true, "_releases": [ { "version": "2024.12.4", "date": "2024-12-08" }, { "version": "2025.1.20", "date": "2025-01-23" }, { "version": "2025.10.21", "date": "2025-10-22" }, { "version": "2026.1.30", "date": "2026-01-30" } ], "_exports": [ "add_power_ci", "add_power_pi", "asymptotic", "eval_power_ci", "eval_power_pi", "glm_nb", "glmm_bnb", "glmm_poisson", "lrt_bnb", "lrt_nb", "mle_bnb_alt", "mle_bnb_null", "mle_nb_alt", "mle_nb_null", "nll_bnb_alt", "nll_bnb_null", "nll_nb_alt", "nll_nb_null", "power", "sim_bnb", "sim_log_lognormal", "sim_nb", "simulated", "t_test_paired", "t_test_welch", "wald_test_bnb", "wald_test_nb" ], "_help": [ { "page": "add_power_ci", "title": "Add confidence intervals for power estimates", "topics": [ "add_power_ci" ] }, { "page": "add_power_pi", "title": "Add Bayesian posterior predictive intervals for power estimates", "topics": [ "add_power_pi" ] }, { "page": "distribution", "title": "Test statistic distribution under the null", "topics": [ "asymptotic", "distribution", "simulated" ] }, { "page": "eval_power_ci", "title": "Evaluate confidence intervals for power estimates", "topics": [ "eval_power_ci" ] }, { "page": "eval_power_pi", "title": "Evaluate Bayesian posterior predictive intervals for power estimates", "topics": [ "eval_power_pi" ] }, { "page": "glm_nb", "title": "GLM for NB ratio of means", "topics": [ "glm_nb" ] }, { "page": "glmm_bnb", "title": "GLMM for BNB ratio of means", "topics": [ "glmm_bnb" ] }, { "page": "glmm_poisson", "title": "GLMM for Poisson ratio of means", "topics": [ "glmm_poisson" ] }, { "page": "lrt_bnb", "title": "Likelihood ratio test for BNB ratio of means", "topics": [ "lrt_bnb" ] }, { "page": "lrt_nb", "title": "Likelihood ratio test for NB ratio of means", "topics": [ "lrt_nb" ] }, { "page": "mle_bnb", "title": "MLE for BNB", "topics": [ "mle_bnb", "mle_bnb_alt", "mle_bnb_null" ] }, { "page": "mle_nb", "title": "MLE for NB", "topics": [ "mle_nb", "mle_nb_alt", "mle_nb_null" ] }, { "page": "nll_bnb", "title": "Negative log-likelihood for BNB", "topics": [ "nll_bnb", "nll_bnb_alt", "nll_bnb_null" ] }, { "page": "nll_nb", "title": "Negative log-likelihood for NB", "topics": [ "nll_nb", "nll_nb_alt", "nll_nb_null" ] }, { "page": "plot.depower", "title": "Plot power objects", "topics": [ "plot.depower" ] }, { "page": "power", "title": "Simulated power", "topics": [ "power" ] }, { "page": "sim_bnb", "title": "Simulate BNB data", "topics": [ "sim_bnb" ] }, { "page": "sim_log_lognormal", "title": "Simulate log-transformed lognormal data", "topics": [ "sim_log_lognormal" ] }, { "page": "sim_nb", "title": "Simulate NB data", "topics": [ "sim_nb" ] }, { "page": "t_test_paired", "title": "Paired and one-sample t-Tests", "topics": [ "t_test_paired" ] }, { "page": "t_test_welch", "title": "Welch's t-Test", "topics": [ "t_test_welch" ] }, { "page": "wald_test_bnb", "title": "Wald test for BNB ratio of means", "topics": [ "wald_test_bnb" ] }, { "page": "wald_test_nb", "title": "Wald test for NB ratio of means", "topics": [ "wald_test_nb" ] } ], "_readme": "https://bitbucket.org/bklamer/depower/raw/HEAD/README.md", "_rundeps": [ "backports", "BH", "boot", "broom", "callr", "charport", "cli", "colorspace", "cowplot", "cpp11", "crayon", "Deriv", "doBy", "dplyr", "farver", "forecast", "fracdiff", "generics", "ggplot2", "glmmTMB", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "mgcv", "minqa", "modelr", "multidplyr", "mvnfast", "nlme", "nloptr", "nnet", "numDeriv", "otel", "pbkrtest", "pillar", "pkgconfig", "processx", "ps", "purrr", "qs2", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "Rdpack", "reformulas", "rlang", "RTMB", "S7", "sandwich", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timeDate", "TMB", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_score": 4.343408593803858, "_indexed": true, "_nocasepkg": "depower", "_universes": [ "bklamer", "bitbucket-bklamer" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2026.11.11", "date": "2026-11-11T18:58:51.000Z", "distro": "resolute", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/672f7f651223bfff2d71001f69d3b7656af94667597aae4a84a7beb33c2a9868", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.6.2", "os": "linux", "version": "2026.11.11", "date": "2026-11-11T18:58:09.000Z", "distro": "resolute", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/03b80856b0ade61e2a9f2d8d3aaa7f975b51918d5a256ac3f78b34c2f147a5fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.5.3", "os": "mac", "version": "2026.11.11", "date": "2026-11-11T18:57:43.000Z", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/45785be8f209ec5ee161ee4fc798a02e9f6a1e55839820bd87f279838a7e850c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.6.2", "os": "mac", "version": "2026.11.11", "date": "2026-11-11T18:57:50.000Z", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/038c1539314b3276d74439eb50d0140bef5fa4618fc0a776102f9a92f575663c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.6.0", "os": "wasm", "version": "2026.11.11", "date": "2026-11-11T18:58:16.000Z", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/e46cd7bea21170d512bf178ddf3f2e5410558d35629100b40a34924f93ac4d50", "status": "success", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.7.0", "os": "win", "version": "2026.11.11", "date": "2026-11-11T18:59:00.000Z", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/266c0a87bba988f0229b8ca35a11b40ab00667705c8e2b5b9d4eb2cd7b01f8e5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.5.3", "os": "win", "version": "2026.11.11", "date": "2026-11-11T18:58:00.000Z", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/35921a47b24366ba0dc9fefe2408e4a5809acbd2dde2c79162b4cc73eb1f83b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" }, { "r": "4.6.2", "os": "win", "version": "2026.11.11", "date": "2026-11-11T18:58:41.000Z", "commit": "b4057e799f40cc7787f2b7cf7ebeb7b8b91f6fb5", "fileid": "https://r2.ropensci.org/28f6d57ffddf7b0dc55448cd24f7ecf9f40cf8ee769dd0d981ec4bf844a31625", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bklamer/actions/runs/43081752069" } ] }