{ "_id": "6a1c08f51d7bb097a0a2c578", "Package": "NBPSeq", "Type": "Package", "Version": "0.3.5", "Date": "05-17-2014", "Title": "Negative Binomial Models for RNA-Sequencing Data", "Author": "Yanming Di , Daniel W Schafer\n, with contributions from Jason S\nCumbie and Jeff H Chang\n.", "Maintainer": "Yanming Di ", "Description": "Negative Binomial (NB) models for two-group comparisons\nand regression inferences from RNA-Sequencing Data.", "License": "GPL-2", "LazyLoad": "yes", "Repository": "https://diystat.r-universe.dev", "Date/Publication": "2014-05-18 00:19:07 UTC", "RemoteUrl": "https://github.com/diystat/nbpseq", "RemoteRef": "HEAD", "RemoteSha": "358f095f4846476c7c9ffe720b502899ea18affb", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-31 10:04:33 UTC", "User": "root" }, "MD5sum": "2d7f8484f09d95914462afaa5164a44d", "_user": "diystat", "_type": "src", "_file": "NBPSeq_0.3.5.tar.gz", "_fileid": "8cddaf512f4698d88ab9d5a7ae42a2c58150c79eaf93350248aa4b0544adb25b", "_filesize": 521471, "_sha256": "8cddaf512f4698d88ab9d5a7ae42a2c58150c79eaf93350248aa4b0544adb25b", "_created": "2026-05-31T10:04:33.000Z", "_published": "2026-05-31T10:09:57.064Z", "_distro": "noble", "_jobs": [ { "job": 78717359762, "time": 133, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7315837085" }, { "job": 78717359794, "time": 96, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7315833207" }, { "job": 78717359786, "time": 109, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7315834672" }, { "job": 78717359759, "time": 113, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7315835075" }, { "job": 78717359782, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7315835754" }, { "job": 78717359775, "time": 282, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7315849512" }, { "job": 78717359779, "time": 183, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7315838226" }, { "job": 78717359787, "time": 271, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7315847116" }, { "job": 78717237564, "time": 131, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7315822678" }, { "job": 78717359747, "time": 97, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7315833183" }, { "job": 78717359751, "time": 76, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7315831186" }, { "job": 78717359750, "time": 67, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7315830135" }, { "job": 78717359757, "time": 82, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7315831763" } ], "_buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/diystat/nbpseq", "_commit": { "id": "358f095f4846476c7c9ffe720b502899ea18affb", "author": "diystat ", "committer": "diystat ", "message": "version 0.3.5\n", "time": 1400372347 }, "_maintainer": { "name": "Yanming Di", "email": "diy@stat.oregonstate.edu", "login": "diystat", "description": "", "uuid": 7268873 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "splines", "role": "Imports" } ], "_owner": "diystat", "_selfowned": true, "_usedby": 3, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "diystat", "count": 13, "uuid": 7268873 } ], "_userbio": { "uuid": 7268873, "type": "user", "name": "Yanming Di" }, "_downloads": { "count": 324, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NBPSeq" }, "_mentions": 32, "_devurl": "https://github.com/diystat/nbpseq", "_searchresults": 17, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NBPSeq.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/diystat/nbpseq", "_realowner": "diystat", "_cranurl": true, "_releases": [ { "version": "0.1.4", "date": "2011-04-24" }, { "version": "0.1.6", "date": "2012-05-26" }, { "version": "0.1.8", "date": "2012-11-19" }, { "version": "0.3.0", "date": "2014-04-14" }, { "version": "0.3.1", "date": "2022-06-09" } ], "_exports": [ "[.nb.data", "[.nb.glm", "binxy", "Cdqrls", "compute.tail.prob", "disp.by.group", "disp.fun.nb2", "disp.fun.nbp", "disp.fun.nbq", "disp.fun.nbs", "disp.fun.step", "disp.nbp", "disp.nbq", "disp.nbs", "disp.predictor.mu", "disp.predictor.pi", "disp.predictor.rs", "disp.step", "estimate.disp", "estimate.dispersion", "estimate.dispersion.by.group", "estimate.norm.factors", "estimate.norm.factors.AH2010", "exact.nb.test", "example.his2d.old", "example.hist2d", "example.smart.plot", "example.table", "filter.mu.pre", "fit.nb.glm", "fit.nb.glm.1", "fit.nb.glm.1u", "get.mean.hat", "get.nbp.pars", "get.rel.mean", "get.var.hat", "hist2d", "hoa.1d", "hoa.hd", "irls.nb", "irls.nb.1", "l.nb", "ll.nb", "log.phi.nb2", "log.phi.nbp", "log.phi.nbq", "ma.plot", "make.disp", "mv.line", "mv.line.fitted", "mv.line.nbp", "mv.plot", "mv.points", "nb.glm.test", "nbp.test", "nll.log.phi.fun", "optim.disp.apl", "optim.disp.pl", "optim.pcl", "phi.line", "phi.line.fitted", "phi.line.nbp", "phi.plot", "plot.nb.data", "plot.nb.dispersion", "plot.nbp", "plot.qvalue", "prepare.nb.data", "prepare.nbp", "print.nb.data", "print.nb.dispersion", "print.nb.test", "print.nbp", "qplot", "qsummary", "qvalue", "qvalue.gui", "qwrite", "smart.plot", "smart.plot.new", "smart.plot.old", "smart.points", "summary.qvalue", "test.coefficient", "test.compute.tail.prob", "thin.counts" ], "_datasets": [ { "name": "arab", "title": "Arabidopsis RNA-Seq Data Set", "object": "arab", "file": "arab.rda", "class": [ "matrix", "array" ], "fields": [ "mock1", "mock2", "mock3", "hrcc1", "hrcc2", "hrcc3" ], "rows": 26222, "table": true, "tojson": true } ], "_help": [ { "page": "NBPSeq-package", "title": "Negative Binomial Regression Models for Statistical Analysis of RNA-Sequencing Data", "topics": [ "NBPSeq-package", "NBPSeq" ] }, { "page": "sub-.nb.data", "title": "hello", "topics": [ "[.nb.data" ] }, { "page": "arab", "title": "Arabidopsis RNA-Seq Data Set", "topics": [ "arab" ] }, { "page": "compute.tail.prob", "title": "(private) Compute the tail probability of a conditional distribution involving a pair of Negative Binomial (NB) random variables given their sum", "topics": [ "compute.tail.prob" ] }, { "page": "disp.by.group", "title": "Specify a dispersion model where the parameters of the model will be estimated separately for different groups", "topics": [ "disp.by.group" ] }, { "page": "disp.nbp", "title": "(private) Specify a NBP dispersion model", "topics": [ "disp.nbp" ] }, { "page": "disp.nbq", "title": "(private) Specify a NBQ dispersion model", "topics": [ "disp.nbq" ] }, { "page": "disp.nbs", "title": "(private) Specify a NBS dispersion model", "topics": [ "disp.nbs" ] }, { "page": "disp.predictor.mu", "title": "Dispersion precitor", "topics": [ "disp.predictor.mu" ] }, { "page": "disp.step", "title": "(private) Specify a piecewise constant dispersion model", "topics": [ "disp.step" ] }, { "page": "disp.fun", "title": "(private) Specify a NB2, NBP, NBS, NBS, or STEP dispersion model", "topics": [ "disp.fun.nb2", "disp.fun.nbp", "disp.fun.nbq", "disp.fun.nbs", "disp.fun.step", "Dispersion Models" ] }, { "page": "estimate.disp", "title": "Fit a parametric disperison model to thinned counts", "topics": [ "estimate.disp" ] }, { "page": "estimate.dispersion", "title": "Estimate Negative Binomial Dispersion", "topics": [ "estimate.dispersion" ] }, { "page": "estimate.norm.factors", "title": "Estiamte Normalization Factors", "topics": [ "estimate.norm.factors" ] }, { "page": "exact.nb.test", "title": "Exact Negative Binomial Test for Differential Gene Expression", "topics": [ "exact.nb.test" ] }, { "page": "filter.mu.pre", "title": "Create a logical vector specifyfing the subset of rows to be used when estimating the dispersion model", "topics": [ "filter.mu.pre" ] }, { "page": "fit.nb.glm.1", "title": "Fit a single negative binomial (NB) log-linear regression model with known dispersion paramreters", "topics": [ "fit.nb.glm.1" ] }, { "page": "fit.nb.glm.1u", "title": "Fit a single negative binomial (NB) log-linear regression model with a common unknown dispersion paramreter", "topics": [ "fit.nb.glm.1u" ] }, { "page": "get.mean.hat", "title": "(private) Extract row means of the pseudo counts for the specified group from an 'nbp' object.", "topics": [ "get.mean.hat" ] }, { "page": "get.nbp.pars", "title": "(private) Retrieve nbp parameters for one of the treatment groups from an nbp object", "topics": [ "get.nbp.pars" ] }, { "page": "get.rel.mean", "title": "(private) Extract row relative means of the pseudo counts for the specified group from an 'nbp' object.", "topics": [ "get.rel.mean" ] }, { "page": "get.var.hat", "title": "(private) Extract estimated variance from the oupput of 'nbp-mcle' or 'nbp-test'", "topics": [ "get.var.hat" ] }, { "page": "hist2d", "title": "2-d Histogram", "topics": [ "hist2d" ] }, { "page": "hoa.1d", "title": "(private) One-dimensional HOA test for a regression coefficient in an NB GLM model", "topics": [ "hoa.1d" ] }, { "page": "hoa.hd", "title": "(private) HOA test for regression coefficients in an NBP GLM model", "topics": [ "hoa.hd" ] }, { "page": "irls.nb", "title": "(private) Estiamte the regression coefficients in an NB GLM model", "topics": [ "irls.nb" ] }, { "page": "irls.nb.1", "title": "Estimate the regression coefficients in an NB GLM model", "topics": [ "irls.nb.1" ] }, { "page": "l.nb", "title": "(private) The Log Likelihood of a NB Model", "topics": [ "l.nb" ] }, { "page": "log.phi.nb2", "title": "(private) A NBP dispersion model", "topics": [ "log.phi.nb2" ] }, { "page": "log.phi.nbp", "title": "(private) A NBP dispersion model", "topics": [ "log.phi.nbp" ] }, { "page": "log.phi.nbq", "title": "(private) A NBQ dispersion model", "topics": [ "log.phi.nbq" ] }, { "page": "ma.plot", "title": "(private) MA plot with differently expressed genes highlighted", "topics": [ "ma.plot" ] }, { "page": "make.disp", "title": "(private) Specify a dispersion model", "topics": [ "make.disp" ] }, { "page": "mv.line", "title": "(private) Overlay an estimated mean-variance line", "topics": [ "mv.line" ] }, { "page": "mv.line.fitted", "title": "(private) Overlay an estimated mean-variance line", "topics": [ "mv.line.fitted" ] }, { "page": "mv.line.nbp", "title": "(private) Overlay a NBP mean-variance line on an existing plot", "topics": [ "mv.line.nbp" ] }, { "page": "mv.plot", "title": "(private) Mean-variance plot", "topics": [ "mv.plot" ] }, { "page": "mv.points", "title": "(private) Highlight a subset of points on the mean-variance plot", "topics": [ "mv.points" ] }, { "page": "nb.glm.test", "title": "Fit Negative Binomial Regression Model and Test for a Regression Coefficient", "topics": [ "nb.glm.test" ] }, { "page": "nbp.test", "title": "NBP Test for Differential Gene Expression from RNA-Seq Counts", "topics": [ "nbp.test" ] }, { "page": "nll.log.phi.fun", "title": "Negative profile conditional likelihood of the dispersion model", "topics": [ "nll.log.phi.fun" ] }, { "page": "optim.disp.apl", "title": "(private) Estimate the parameters in a dispersion model", "topics": [ "optim.disp.apl" ] }, { "page": "optim.disp.pl", "title": "(private) Estimate the parameters in a dispersion model", "topics": [ "optim.disp.pl" ] }, { "page": "phi.line", "title": "(private) Overlay an mean-dispersion line on an esimtated plot", "topics": [ "phi.line" ] }, { "page": "phi.line.fitted", "title": "(private) Overlay an estimated mean-dispersion line on an existing plot", "topics": [ "phi.line.fitted" ] }, { "page": "phi.line.nbp", "title": "(private) Overlay an estimated mean-dispersion line on an existing plot", "topics": [ "phi.line.nbp" ] }, { "page": "phi.plot", "title": "Plot estimated genewise NB2 dispersion parameter versus estimated mean", "topics": [ "phi.plot" ] }, { "page": "plot.nb.data", "title": "Boxplot and scatterplot matrix of relative frequencies (after normalization)", "topics": [ "plot.nb.data" ] }, { "page": "plot.nb.dispersion", "title": "Plot the estimated dispersion as a function of the preliminarily estimated mean relative frequencies", "topics": [ "plot.nb.dispersion" ] }, { "page": "plot.nbp", "title": "Diagnostic Plots for an NBP Object", "topics": [ "plot.nbp" ] }, { "page": "prepare.nb.data", "title": "Prepare the NB Data Structure for RNA-Seq Read Counts", "topics": [ "prepare.nb.data" ] }, { "page": "prepare.nbp", "title": "Prepare the Data Structure for Exact NB test for Two-Group Comparison", "topics": [ "prepare.nbp" ] }, { "page": "print.nb.data", "title": "Print summary of the nb counts", "topics": [ "print.nb.data" ] }, { "page": "print.nb.dispersion", "title": "Print the estimated dispersion model", "topics": [ "print.nb.dispersion" ] }, { "page": "print.nb.test", "title": "Print output from 'test.coefficient'", "topics": [ "print.nb.test" ] }, { "page": "print.nbp", "title": "Print summary of an NBP Object", "topics": [ "print.nbp" ] }, { "page": "smart.plot.new", "title": "(private) An alternative to plot.default() for plotting a large number of densely distributed points.", "topics": [ "smart.plot.new" ] }, { "page": "smart.plot.old", "title": "(private) An alternative to plot.default() for plotting a large number of densely distributed points.", "topics": [ "smart.plot.old" ] }, { "page": "smart.points", "title": "(private) An alternative to point.default() for plotting a large number of densely distributed points.", "topics": [ "smart.points" ] }, { "page": "test.coefficient", "title": "Large-sample Test for a Regression Coefficient in an Negative Binomial Regression Model", "topics": [ "test.coefficient" ] }, { "page": "thin.counts", "title": "(private) Thin (downsample) counts to make the effective library sizes equal.", "topics": [ "thin.counts" ] } ], "_readme": "https://github.com/diystat/nbpseq/raw/HEAD/README.md", "_rundeps": [], "_score": 4.883661435153618, "_indexed": true, "_nocasepkg": "nbpseq", "_universes": [ "diystat" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.5", "date": "2026-05-31T10:06:56.000Z", "distro": "noble", "arch": "aarch64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "ab68939f82e12d3503b86a6d6b4f05854696945c1f60628f80e48bb48ff0b08a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.7.0", "os": "linux", "version": "0.3.5", "date": "2026-05-31T10:06:16.000Z", "distro": "noble", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "98e444f8b036f51752d2a801f4220f76f70457c8b18736bd8f7658b61d1132e0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.6.0", "os": "linux", "version": "0.3.5", "date": "2026-05-31T10:06:32.000Z", "distro": "noble", "arch": "aarch64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "304fe76cc70702bfa64bcef8b1edd797e64c39e7f157606a8205cc7d279303e3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.6.0", "os": "linux", "version": "0.3.5", "date": "2026-05-31T10:06:32.000Z", "distro": "noble", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "de3536f978e87235793f573c9f67bad3fe0fca297202b354eb9ec951f5d2579b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.5.3", "os": "mac", "version": "0.3.5", "date": "2026-05-31T10:06:41.000Z", "arch": "aarch64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "7c9bf861d052c2a4fe27416dc4e5a50e4c8f8a294dce8d9148d246c61be0e889", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.5.3", "os": "mac", "version": "0.3.5", "date": "2026-05-31T10:08:44.000Z", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "38fe213ef9ef3c3499c231fb022d2ab8867e94defc706b6ef374a7b4c29c613a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.6.0", "os": "mac", "version": "0.3.5", "date": "2026-05-31T10:06:59.000Z", "arch": "aarch64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "2b0ee711e435b4f1346088f2eec1318b0e8a45da1b7ad0159d118248db2511a0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.6.0", "os": "mac", "version": "0.3.5", "date": "2026-05-31T10:08:25.000Z", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "0f2978227bfaf34720949951c9204473f155bd68cbbd434fc28152435426be43", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.5", "date": "2026-05-31T10:06:30.000Z", "arch": "emscripten", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "03ba65cf98ca891e285f4ea984869e2443d8f354a58e49f15abf28a9a0b0812d", "status": "success", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.7.0", "os": "win", "version": "0.3.5", "date": "2026-05-31T10:05:50.000Z", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "e523f938b50e8911854f2645250785af1853e9563bcaa3e7093ae45514274c20", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.5.3", "os": "win", "version": "0.3.5", "date": "2026-05-31T10:05:36.000Z", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "145a47e08635e12f7e1111b9e11215e5e2160ef80dd826b885968ef70d286181", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" }, { "r": "4.6.0", "os": "win", "version": "0.3.5", "date": "2026-05-31T10:05:50.000Z", "arch": "x86_64", "commit": "358f095f4846476c7c9ffe720b502899ea18affb", "fileid": "80f2c6eb90cf49a5d3f99cbb9a1be635237263fe91c95d19f3b10df2ea4aa3f4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/diystat/actions/runs/26709600421" } ] }