{ "_id": "6a1418bbacfb0bcc41d3cc1a", "Package": "EZbakR", "Title": "Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq\nData", "Version": "0.2.0", "Authors@R": "person(given = \"Isaac\",\nfamily = \"Vock\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"isaac.vock@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7178-6886\"))", "Description": "A complete rewrite and reimagining of 'bakR' (see 'Vock et\nal.' (2025) ). Designed to\nsupport a wide array of analyses of nucleotide recoding RNA-seq\n(NR-seq) datasets of any type, including\nTimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq),\nTT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR'\nextends standard NR-seq standard NR-seq mutational modeling to\nsupport multi-label analyses (e.g., 4sU and 6sG dual labeling),\nand implements an improved hierarchical model to better account\nfor transcript-to-transcript variance in metabolic label\nincorporation. 'EZbakR' also generalized dynamical systems\nmodeling of NR-seq data to support analyses of premature mRNA\nprocessing and flow between subcellular compartments. Finally,\n'EZbakR' implements flexible and well-powered comparative\nanalyses of all estimated parameters via design\nmatrix-specified generalized linear modeling.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "biocViews": "", "LazyData": "true", "VignetteBuilder": "knitr", "URL": "https://isaacvock.github.io/EZbakR/,\nhttps://github.com/isaacvock/EZbakR", "BugReports": "https://github.com/isaacvock/EZbakR/issues", "Config/pak/sysreqs": "cmake libicu-dev libssl-dev", "Repository": "https://isaacvock.r-universe.dev", "Date/Publication": "2026-01-25 02:22:38 UTC", "RemoteUrl": "https://github.com/isaacvock/ezbakr", "RemoteRef": "HEAD", "RemoteSha": "dd3e89ee7867330b31584455455a0380f32a61c7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 09:34:47 UTC", "User": "root" }, "Author": "Isaac Vock [aut, cre, cph] (ORCID:\n)", "Maintainer": "Isaac Vock ", "MD5sum": 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metadf", "object": "example_metadf", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sample", "tl", "genotype" ], "rows": 6, "table": true, "tojson": true }, { "name": "ode_models", "title": "Example ODE model graphs and formulas", "object": "ode_models", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "standard_fraction_design", "title": "Standard 'fraction_design' table for 'EstimateFractions'", "object": "standard_fraction_design", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "TC", "present" ], "rows": 2, "table": true, "tojson": true }, { "name": "tilac_fraction_design", "title": "TILAC 'fraction_design' table for 'EstimateFractions'", "object": "tilac_fraction_design", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "TC", "GA", "present" ], "rows": 4, "table": true, "tojson": true } ], "_help": [ { "page": "AverageAndRegularize", "title": "Average parameter estimates across replicates, and regularize variance estimates", "topics": [ "AverageAndRegularize" ] }, { "page": "CompareParameters", "title": "Get contrasts of estimated parameters", "topics": [ "CompareParameters" ] }, { "page": "CorrectDropout", "title": "Correct for experimental/bioinformatic dropout of labeled RNA.", "topics": [ "CorrectDropout" ] }, { "page": "create_fraction_design", "title": "Generate a 'fraction_design' table for 'EstimateFractions'.", "topics": [ "create_fraction_design" ] }, { "page": "DeconvolveFractions", "title": "Deconvolve multi-feature fractions.", "topics": [ "DeconvolveFractions" ] }, { "page": "EstimateFractions", "title": "Estimate fractions of each RNA population.", "topics": [ "EstimateFractions", "EstimateFractions.EZbakRArrowData", "EstimateFractions.EZbakRData" ] }, { "page": "EstimateIsoformFractions", "title": "Estimate isoform-specific fraction news (or more generally \"fractions\").", "topics": [ "EstimateIsoformFractions" ] }, { "page": "EstimateKinetics", "title": "Estimate kinetic parameters", "topics": [ "EstimateKinetics" ] }, { "page": "EstimateMutRates", "title": "Estimate mutation rates", "topics": [ "EstimateMutRates", "EstimateMutRates.EZbakRArrowData", "EstimateMutRates.EZbakRData" ] }, { "page": "example_cB", "title": "Example cB table", "topics": [ "example_cB" ] }, { "page": "example_metadf", "title": "Example metadf", "topics": [ "example_metadf" ] }, { "page": "EZbakRArrowData", "title": "'EZbakRArrowData' object helper function for users", "topics": [ "EZbakRArrowData" ] }, { "page": "EZbakRData", "title": "'EZbakRData' object helper function for users", "topics": [ "EZbakRData" ] }, { "page": "EZbakRFractions", "title": "'EZbakRFractions' helper function for users", "topics": [ "EZbakRFractions" ] }, { "page": "EZbakRKinetics", "title": "'EZbakRKinetics' helper function for users", "topics": [ "EZbakRKinetics" ] }, { "page": "EZDynamics", "title": "Generalized dynamical systems modeling", "topics": [ "EZDynamics" ] }, { "page": "EZget", "title": "Easily get EZbakR table of estimates of interest", "topics": [ "EZget" ] }, { "page": "EZMAPlot", "title": "Make an MAPlot from EZbakR comparison", "topics": [ "EZMAPlot" ] }, { "page": "EZpcaPlot", "title": "Make an MAPlot from EZbakR comparison", "topics": [ "EZpcaPlot" ] }, { "page": "EZQC", "title": "Run quality control checks", "topics": [ "EZQC" ] }, { "page": "EZQC.EZbakRArrowData", "title": "Run quality control checks", "topics": [ "EZQC.EZbakRArrowData" ] }, { "page": "EZQC.EZbakRData", "title": "Run quality control checks", "topics": [ "EZQC.EZbakRData" ] }, { "page": "EZQC.EZbakRFractions", "title": "Run quality control checks", "topics": [ "EZQC.EZbakRFractions" ] }, { "page": "EZSimulate", "title": "Simulate NR-seq data for multiple replicates of multiple biological conditions", "topics": [ "EZSimulate" ] }, { "page": "EZVolcanoPlot", "title": "Make a VolcanoPlot from EZbakR comparison", "topics": [ "EZVolcanoPlot" ] }, { "page": "get_normalized_read_counts", "title": "Get normalized read counts from either a cB table or 'EZbakRFractions' object.", "topics": [ "get_normalized_read_counts", "get_normalized_read_counts.EZbakRData", "get_normalized_read_counts.EZbakRFractions" ] }, { "page": "ImportIsoformQuant", "title": "Import transcript isoform quantification into EZbakRData object", "topics": [ "ImportIsoformQuant" ] }, { "page": "new_EZbakRArrowData", "title": "'EZbakRArrowData' object constructor for internal use", "topics": [ "new_EZbakRArrowData" ] }, { "page": "new_EZbakRData", "title": "'EZbakRDataobject' constructor for internal use", "topics": [ "new_EZbakRData" ] }, { "page": "new_EZbakRFractions", "title": "'EZbakRFractions' object constructor", "topics": [ "new_EZbakRFractions" ] }, { "page": "new_EZbakRKinetics", "title": "'EZbakRKinetics' object constructor", "topics": [ "new_EZbakRKinetics" ] }, { "page": "NormalizeForDropout", "title": "Normalize for experimental/bioinformatic dropout of labeled RNA.", "topics": [ "NormalizeForDropout" ] }, { "page": "ode_models", "title": "Example ODE model graphs and formulas", "topics": [ "ode_models" ] }, { "page": "print.EZbakRArrowData", "title": "Print method for 'EZbakRArrowData' objects", "topics": [ "print.EZbakRArrowData" ] }, { "page": "print.EZbakRData", "title": "Print method for 'EZbakRData' objects", "topics": [ "print.EZbakRData" ] }, { "page": "SimpleSim", "title": "Simple simulation function", "topics": [ "SimpleSim" ] }, { "page": "SimulateDynamics", "title": "Simulation of generalized dynamical system model.", "topics": [ "SimulateDynamics" ] }, { "page": "SimulateIsoforms", "title": "Simulation of transcript isoform kinetic parameters.", "topics": [ "SimulateIsoforms" ] }, { "page": "SimulateMultiCondition", "title": "Simulate NR-seq data for multiple replicates of multiple biological conditions", "topics": [ "SimulateMultiCondition" ] }, { "page": "SimulateMultiLabel", "title": "Simulate one replicate of multi-label NR-seq data", "topics": [ "SimulateMultiLabel" ] }, { "page": "SimulateOneRep", "title": "Simulate a single replicate of NR-seq data", "topics": [ "SimulateOneRep" ] }, { "page": "standard_fraction_design", "title": "Standard 'fraction_design' table for 'EstimateFractions'", "topics": [ "standard_fraction_design" ] }, { "page": "tilac_fraction_design", "title": "TILAC 'fraction_design' table for 'EstimateFractions'", "topics": [ "tilac_fraction_design" ] }, { "page": "validate_EZbakRArrowData", "title": "'EZbakRArrowData' EZbakRArrowData validator", "topics": [ "validate_EZbakRArrowData" ] }, { "page": "validate_EZbakRData", "title": "'EZbakRDataobject' validator", "topics": [ "validate_EZbakRData" ] }, { "page": "validate_EZbakRFractions", "title": "'EZbakRFractions' object validator", "topics": [ "validate_EZbakRFractions" ] }, { "page": "validate_EZbakRKinetics", "title": "'EZbakRKinetics' object validator", "topics": [ "validate_EZbakRKinetics" ] }, { "page": "VectSimulateMultiLabel", "title": "Vectorized simulation of one replicate 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