Package: Tweedieverse
Title: Differential Analysis of Omics Data Based on the Tweedie
        Distribution
Version: 0.99.0
Date: 2026-05-07
Authors@R: c(
  person("Nalin", "Arora", email = "naa4050@med.cornell.edu", role = c("aut", "ctb", "cre"), comment = c(ORCID = "0009-0009-1340-688X")),
  person("Ziyu", "Liu", email = "lclcencen@gmail.com", role = "ctb"),
  person("Ali", "Rahnavard", email = "gholamali.rahnavard@gmail.com", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-9710-0248")),
  person("Himel", "Mallick", email = "him4004@med.cornell.edu", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-4956-2429"))
  )
Description: A toolkit for differential analysis of omics data.
        Implements a CPLM-based statistical workflow built on the
        Tweedie distribution. Unlike traditional single-omics tools,
        Tweedieverse is technology-agnostic and can be applied to both
        count and continuous measurements arising from diverse
        high-throughput technologies (e.g. transcript abundances from
        bulk and single-cell RNA-Seq studies in the form of UMI counts
        or non-UMI counts, microbiome taxonomic and functional profiles
        in the form of counts or relative abundances, and compound
        abundance levels or peak intensities from metabolomics and
        other mass spectrometry-based experiments, among others). The
        software includes multiple customization options such as the
        inclusion of random effects and multiple covariates along with
        several data exploration capabilities and visualization modules
        in a unified estimation umbrella.
Depends: R (>= 4.5.0)
Imports: cplm, glmmTMB, BiocParallel, logging, dplyr, ggplot2,
        pheatmap, cowplot, SummarizedExperiment, statmod, Maaslin2,
        edgeR, scran, SingleCellExperiment, TreeSummarizedExperiment,
        MultiAssayExperiment
Suggests: airway, data.table, knitr, rmarkdown, BiocStyle, muscat,
        testthat
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
VignetteBuilder: knitr
URL: https://github.com/himelmallick/Tweedieverse
BugReports: https://github.com/himelmallick/Tweedieverse/issues
biocViews: DifferentialExpression, Software, Visualization,
        CellBasedAssays, ATACSeq, Microbiome, MassSpectrometry,
        SingleCell, Metabolomics, Metagenomics, WorkflowStep,
        MultipleComparison, Normalization, Regression, RNASeq
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-28 16:58:52 UTC
RemoteUrl: https://github.com/BiocStaging/Tweedieverse
RemoteRef: HEAD
RemoteSha: a7e3890c120c8e4b166e1c558f9066798620335c
NeedsCompilation: no
Packaged: 2026-09-28 22:22:35 UTC; root
Author: Nalin Arora [aut, ctb, cre] (ORCID:
    <https://orcid.org/0009-0009-1340-688X>),
  Ziyu Liu [ctb],
  Ali Rahnavard [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-9710-0248>),
  Himel Mallick [aut, ctb] (ORCID:
    <https://orcid.org/0000-0003-4956-2429>)
Maintainer: Nalin Arora <naa4050@med.cornell.edu>