Package: scShapes
Type: Package
Title: A Statistical Framework for Modeling and Identifying
        Differential Distributions in Single-cell RNA-sequencing Data
Version: 1.16.0
Authors@R: person("Malindrie", "Dharmaratne", role = c("cre", "aut"), 
                  email = "malindrie@gmail.com", 
                  comment = c(ORCID = "0000-0002-1694-6496"))
Description: We present a novel statistical framework for identifying 
        differential distributions in single-cell RNA-sequencing 
        (scRNA-seq) data between treatment conditions by modeling gene 
        expression read counts using generalized linear models (GLMs). 
        We model each gene independently under each treatment condition 
        using error distributions Poisson (P), Negative Binomial (NB), 
        Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) 
        with log link function and model based normalization for differences 
        in sequencing depth. Since all four distributions considered in 
        our framework belong to the same family of distributions, 
        we first perform a Kolmogorov-Smirnov (KS) test to select genes 
        belonging to the family of ZINB distributions. Genes passing the 
        KS test will be then modeled using GLMs. Model selection is done 
        by calculating the Bayesian Information Criterion (BIC) and likelihood 
        ratio test (LRT) statistic. 
NeedsCompilation: yes
Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
        emdbook, magrittr, utils
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
URL: https://github.com/Malindrie/scShapes
BugReports: https://github.com/Malindrie/scShapes/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: RNASeq, SingleCell, MultipleComparison, GeneExpression
Depends: R (>= 4.1)
git_url: https://git.bioconductor.org/packages/scShapes
git_branch: RELEASE_3_22
git_last_commit: 8def801
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
Packaged: 2025-10-30 05:24:17 UTC; biocbuild
Author: Malindrie Dharmaratne [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-1694-6496>)
Maintainer: Malindrie Dharmaratne <malindrie@gmail.com>
Built: R 4.5.1; ; 2025-10-30 12:38:33 UTC; unix
