Package: mehenDi
Title: Differential testing on the forest of trees output form TreeTerminus
Version: 0.99.2
Authors@R: c(
    person("Noor Pratap", "Singh", email="noorpratap@gmail.com", 
      role = c("aut", "cre")),
    person("Michael", "Love", email="michaelisaiahlove@gmail.com", 
      role = c("aut", "ctb")),
    person("Rob", "Pato", email="rob@cs.umd.edu", 
      role = c("aut", "ctb"))
    )
Maintainer: Noor Pratap Singh <noorpratap@gmail.com>
URL: https://github.com/NPSDC/mehenDi
Description: This package provides a tree based differential testing for RNA-Seq data,
  where the tree is obtained from \strong{TreeTerminus}. The candidate nodes can
  consist of both leaves and inner nodes, with inner nodes comprising a susbet of 
  transcripts that exhibit high uncertainty.
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews:
    SummarizedExperiment,
    TreeSummarizedExperiment,
    fishpond,
    S4Vectors
Imports:
    SummarizedExperiment,
    TreeSummarizedExperiment,
    phangorn,
    methods,
    matrixStats,
    svMisc,
    Matrix,
    fishpond,
    S4Vectors,
    parallel,
    stats,
    abind,
    beaveR
Remotes:
  NPSDC/beaveR,
  NPSDC/brainSimSmall
Suggests: 
    testthat (>= 3.0.0),
    knitr,
    tximeta,
    org.Hs.eg.db,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    plyranges,
    ggtree,
    grid,
    ggplotify,
    ggplot2,
    ggpubr,
    ape,
    tibble,
    dplyr,
    tidytree,
    plotgardener,
    brainSimSmall,
    rmarkdown
Config/testthat/edition: 3
