Package: TSENAT
Type: Package
Title: Tsallis Entropy Analysis Toolbox
Version: 0.99.0
Authors@R: person(given = "Cristóbal", family = "Gallardo", role = c("aut", "cre"), email = "gallardoalba@pm.me", comment=c(ORCID="0000-0002-5752-2155"))
Description: Quantifies and models isoform-usage complexity in RNA-seq data using 
    Tsallis entropy, a scale-dependent diversity measure. By tuning the entropic index 
    parameter (q), TSENAT examines transcriptome heterogeneity at different scales: 
    rare variants (low q) or dominant isoforms (high q). It enables 
    computing Tsallis entropy and Tsallis divergence from transcript-level estimates, 
    comparing measures between conditions, testing for differences, and visualizing 
    scale-dependent complexity via q-curves.
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.3
Depends: R (>= 4.5.0)
Imports: SummarizedExperiment, methods, stats, ggplot2, withr,
        BiocParallel, matrixStats, mgcv, geepack, pheatmap, cowplot,
        dplyr, tidyr, S4Vectors, rlang, Rcpp, memoise, digest, readr
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, knitr, rmarkdown, kableExtra, patchwork, covr,
        RColorBrewer, gamsel, glmmTMB, glmnet, gridExtra, nlme,
        fdrtool, MASS, SplicingFactory, devtools, microbenchmark
VignetteBuilder: knitr
URL: https://gallardoalba.github.io/TSENAT
BugReports: https://github.com/gallardoalba/TSENAT/issues
biocViews: Transcriptomics, RNASeq, DifferentialSplicing,
        AlternativeSplicing, TranscriptomeVariant, GeneExpression,
        DifferentialExpression
NeedsCompilation: yes
Packaged: 2026-05-04 17:08:55 UTC; pkgbuild
Author: Cristóbal Gallardo [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5752-2155>)
Maintainer: Cristóbal Gallardo <gallardoalba@pm.me>
