FracFixR: Compositional Statistical Framework for RNA Fractionation Analysis (original) (raw)
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.
| Version: | 1.0.0 |
|---|---|
| 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 |
| Published: | 2025-10-21 |
| DOI: | 10.32614/CRAN.package.FracFixR |
| Author: | Alice Cleynen  [aut, cre], Agin Ravindran [aut], Nikolay Shirokikh [aut] |
| Maintainer: | Alice Cleynen <alice.cleynen at cnrs.fr> |
| License: | CC BY 4.0 |
| NeedsCompilation: | no |
| Materials: | NEWS |
| CRAN checks: | FracFixR results |
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