Package: distinct
Type: Package
Title: distinct: a method for differential analyses via hierarchical
        permutation tests
Version: 1.23.0
Author: Simone Tiberi [aut, cre].
Maintainer: Simone Tiberi <simone.tiberi@uzh.ch>
Description: distinct is a statistical method to perform differential
        testing between two or more groups of distributions;
        differential testing is performed via hierarchical
        non-parametric permutation tests on the cumulative distribution
        functions (cdfs) of each sample. While most methods for
        differential expression target differences in the mean
        abundance between conditions, distinct, by comparing full cdfs,
        identifies, both, differential patterns involving changes in
        the mean, as well as more subtle variations that do not involve
        the mean (e.g., unimodal vs. bi-modal distributions with the
        same mean). distinct is a general and flexible tool: due to its
        fully non-parametric nature, which makes no assumptions on how
        the data was generated, it can be applied to a variety of
        datasets. It is particularly suitable to perform differential
        state analyses on single cell data (i.e., differential analyses
        within sub-populations of cells), such as single cell RNA
        sequencing (scRNA-seq) and high-dimensional flow or mass
        cytometry (HDCyto) data. To use distinct one needs data from
        two or more groups of samples (i.e., experimental conditions),
        with at least 2 samples (i.e., biological replicates) per
        group.
biocViews: Genetics, RNASeq, Sequencing, DifferentialExpression,
        GeneExpression, MultipleComparison, Software, Transcription,
        StatisticalMethod, Visualization, SingleCell, FlowCytometry,
        GeneTarget
License: GPL (>= 3)
Depends: R (>= 4.3)
Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment,
        methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2,
        limma, scater
Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++17
VignetteBuilder: knitr
RoxygenNote: 7.2.3
ByteCompile: true
URL: https://github.com/SimoneTiberi/distinct
BugReports: https://github.com/SimoneTiberi/distinct/issues
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libharfbuzz-dev libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libwebp-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:58:17 UTC
RemoteUrl: https://github.com/bioc/distinct
RemoteRef: HEAD
RemoteSha: fecbaaceb8e6d8a6f5b9ae29459ea03f4a674fc5
NeedsCompilation: yes
Packaged: 2026-01-09 21:15:25 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2026-01-09 21:21:58 UTC; windows
Archs: x64
