Package: postexportKinetics
Title: Kinetic Model Comparison for Post-Export RNA Conversion
Version: 0.99.0
Authors@R: c(
    person("Luca", "Faretra", role = "aut"),
    person("Francesco", "Napolitano", role = "aut"),
    person("Massimo", "Pancione", role = "aut"),
    person("Luigi", "Cerulo", email = "lcerulo@unisannio.it",
           role = c("aut", "cre")))
Description: Compartment-resolved four-state kinetic modelling of
        nuclear and cytoplasmic, unprocessed and processed RNA.
        Implements a constrained nested-model comparison between a null
        model without a post-export conversion rate and a full model
        with a non-negative post-export conversion rate, using
        trapezoidal interval balances, propagated and regularised
        measurement covariance, whitened non-negative least squares and
        a replicate-level generative bootstrap with an add-one p-value.
        Also provides simulation with the manuscript simulator and
        assay-noise models, diagnostic comparison of sampling designs
        with the manuscript benchmark, multiple-testing adjustment,
        exploratory candidate ranking, tidy result tables and plots.
        The post-export conversion rate is a phenomenological parameter
        and does not identify a specific molecular mechanism.
License: MIT + file LICENSE
URL: https://github.com/bioinformatics-sannio/postexportKinetics
BugReports: https://github.com/bioinformatics-sannio/postexportKinetics/issues
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.1.0)
Imports: deSolve, ggplot2 (>= 3.4.0), MASS, nnls, stats,
        SummarizedExperiment, utils
Suggests: expm, knitr, rmarkdown, testthat (>= 3.1.7)
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Software, Transcriptomics, RNASeq, AlternativeSplicing,
        TimeCourse, StatisticalMethod, MultipleComparison,
        Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-26 11:05:44 UTC
RemoteUrl: https://github.com/BiocStaging/postexportKinetics
RemoteRef: HEAD
RemoteSha: d099ac79d1bacc8edd24a5d9aa4f3ffaea67ee0f
NeedsCompilation: no
Packaged: 2026-09-26 13:23:46 UTC; root
Author: Luca Faretra [aut],
  Francesco Napolitano [aut],
  Massimo Pancione [aut],
  Luigi Cerulo [aut, cre]
Maintainer: Luigi Cerulo <lcerulo@unisannio.it>