Package: DifferentialRegulation
Type: Package
Title: Differentially regulated genes from scRNA-seq data
Version: 2.9.0
Description: DifferentialRegulation is a method for detecting
        differentially regulated genes between two groups of samples
        (e.g., healthy vs. disease, or treated vs. untreated samples),
        by targeting differences in the balance of spliced and
        unspliced mRNA abundances, obtained from single-cell
        RNA-sequencing (scRNA-seq) data. From a mathematical point of
        view, DifferentialRegulation accounts for the sample-to-sample
        variability, and embeds multiple samples in a Bayesian
        hierarchical model. Furthermore, our method also deals with two
        major sources of mapping uncertainty: i) 'ambiguous' reads,
        compatible with both spliced and unspliced versions of a gene,
        and ii) reads mapping to multiple genes. In particular,
        ambiguous reads are treated separately from spliced and
        unsplced reads, while reads that are compatible with multiple
        genes are allocated to the gene of origin. Parameters are
        inferred via Markov chain Monte Carlo (MCMC) techniques
        (Metropolis-within-Gibbs).
Authors@R: c(person(given = "Simone",
           family = "Tiberi",
           role = c("aut", "cre"),
           email = "simone.tiberi@unibo.it",
           comment = c(ORCID = "0000-0002-3054-9964")),
           person(given = "Charlotte", family = "Soneson", 
           role = c("aut"),
           email = "charlottesoneson@gmail.com",
           comment = c(ORCID = "0000-0003-3833-2169")))
biocViews: DifferentialSplicing, Bayesian, Genetics, RNASeq,
        Sequencing, DifferentialExpression, GeneExpression,
        MultipleComparison, Software, Transcription, StatisticalMethod,
        Visualization, SingleCell, GeneTarget
License: GPL-3
Depends: R (>= 4.3.0)
Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel,
        foreach, stats, BANDITS, Matrix, SingleCellExperiment,
        SummarizedExperiment, ggplot2, tximport, gridExtra
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat, BiocStyle
SystemRequirements: C++17
VignetteBuilder: knitr
RoxygenNote: 7.3.2
ByteCompile: true
Encoding: UTF-8
URL: https://github.com/SimoneTiberi/DifferentialRegulation
BugReports: https://github.com/SimoneTiberi/DifferentialRegulation/issues
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:16:49 UTC
RemoteUrl: https://github.com/bioc/DifferentialRegulation
RemoteRef: HEAD
RemoteSha: e4187ce3de0c49dfee9413d38dcad7b1c4c12f58
NeedsCompilation: yes
Packaged: 2026-01-16 22:01:21 UTC; root
Author: Simone Tiberi [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3054-9964>),
  Charlotte Soneson [aut] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>)
Maintainer: Simone Tiberi <simone.tiberi@unibo.it>
Built: R 4.6.0; aarch64-apple-darwin23; 2026-01-16 22:04:53 UTC; unix
