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)
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:10:49 UTC
RemoteUrl: https://github.com/bioc/scShapes
RemoteRef: RELEASE_3_22
RemoteSha: 8def801c6a2f4de31d67d4f8ed20933f8aeb5461
Packaged: 2025-11-11 17:34:59 UTC; root
Author: Malindrie Dharmaratne [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-1694-6496>)
Maintainer: Malindrie Dharmaratne <malindrie@gmail.com>
Built: R 4.5.2; ; 2025-11-11 17:38:00 UTC; windows
