Package: DifferentialRegulation
Type: Package
Title: Differentially regulated genes from scRNA-seq data
Version: 1.2.2
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.
  DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model.
  In particular, when reads are compatible with multiple genes or multiple splicing versions of a gene (unspliced spliced or ambiguous), 
  the method allocates these multi-mapping reads to the gene of origin and their splicing version.
  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@uzh.ch",
           comment = c(ORCID = "0000-0002-3054-9964")))
biocViews: DifferentialSplicing, Bayesian, Genetics, RNASeq,
        Sequencing, DifferentialExpression, GeneExpression,
        MultipleComparison, Software, Transcription, StatisticalMethod,
        Visualization, SingleCell, GeneTarget
License: GPL-3
Depends: R (>= 4.2.0)
Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel,
        foreach, stats, BANDITS, Matrix, SingleCellExperiment,
        SummarizedExperiment, ggplot2
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat, BiocStyle
SystemRequirements: C++11
VignetteBuilder: knitr
RoxygenNote: 7.2.0
ByteCompile: true
URL: https://github.com/SimoneTiberi/DifferentialRegulation
BugReports: https://github.com/SimoneTiberi/DifferentialRegulation/issues
git_url: https://git.bioconductor.org/packages/DifferentialRegulation
git_branch: RELEASE_3_16
git_last_commit: 0ae1b53
git_last_commit_date: 2023-01-19
Date/Publication: 2023-01-19
NeedsCompilation: yes
Packaged: 2023-01-19 23:13:58 UTC; biocbuild
Author: Simone Tiberi [aut, cre] (<https://orcid.org/0000-0002-3054-9964>)
Maintainer: Simone Tiberi <simone.tiberi@uzh.ch>
Built: R 4.2.2; x86_64-w64-mingw32; 2023-01-20 12:40:23 UTC; windows
ExperimentalWindowsRuntime: ucrt
Archs: x64
