Package: FracFixR
Type: Package
Title: Compositional Statistical Framework for RNA Fractionation
        Analysis
Version: 1.0.0
Date: 2025-10-16
Authors@R: c(
    person("Alice", "Cleynen", email = "alice.cleynen@cnrs.fr", 
           role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8083-0204")),
    person("Agin", "Ravindran", role = "aut"),
    person("Nikolay", "Shirokikh", email = "nikolay.shirokikh@uwa.edu.au", 
           role = "aut", comment = c(ORCID = "0000-0001-8249-358X")))
Description: A compositional statistical framework for absolute proportion 
    estimation between fractions in RNA sequencing data. 'FracFixR' addresses 
    the fundamental challenge in fractionated RNA-seq experiments where library 
    preparation and sequencing depth obscure the original proportions of RNA 
    fractions. It reconstructs original fraction proportions using non-negative 
    linear regression, estimates the "lost" unrecoverable fraction, corrects 
    individual transcript frequencies, and performs differential proportion 
    testing between conditions. Supports any RNA fractionation protocol including
    polysome profiling, sub-cellular localization, and RNA-protein complex isolation.
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
Imports: future.apply (>= 1.8.1), nnls (>= 1.4), ggplot2 (>= 3.3.5),
        dplyr (>= 1.0.7), RColorBrewer (>= 1.1-2), tidyr (>= 1.1.3),
        matrixStats (>= 0.60.0), aod (>= 1.3.1), stats, utils, future,
        grDevices
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
RoxygenNote: 7.3.2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-10-16 02:59:56 UTC; acleynen
Author: Alice Cleynen [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8083-0204>),
  Agin Ravindran [aut],
  Nikolay Shirokikh [aut] (ORCID:
    <https://orcid.org/0000-0001-8249-358X>)
Maintainer: Alice Cleynen <alice.cleynen@cnrs.fr>
Repository: CRAN
Date/Publication: 2025-10-21 17:40:02 UTC
Built: R 4.6.0; ; 2026-04-26 18:24:38 UTC; unix
