Package: scCompoundDE
Type: Package
Title: Compositional and Transcriptional Decomposition of Pseudo-Bulk
        Differential Expression
Version: 0.99.1
Authors@R: c(
    person("Subhadip", "Jana", role = c("aut", "cre"),
           email = "subhadipjana1409@gmail.com",
           comment = c(ORCID = "0009-0003-7860-2853")))
Description: 
    scCompoundDE decomposes pseudo-bulk differential expression (DE) signals
    into two orthogonal components: transcriptional changes (cell-intrinsic
    expression shifts) and compositional changes (shifts in the relative
    abundance of cell subtypes). Standard pseudo-bulk DE tools confound these
    two sources of signal, producing spurious DE calls when subtype proportions
    differ between conditions. scCompoundDE fits per-subtype limma-voom models,
    estimates subtype proportion shifts, and uses a z-score-normalized
    decomposition to assign each gene a TC_ratio score — the fraction of its
    DE signal attributable to transcription versus composition. Genes are then
    classified as transcriptional (real biology), compositional (artifact), or
    mixed (requires caution). All functions operate natively on
    SingleCellExperiment objects and return a CDEResult S4 object that
    extends the standard DE output with full decomposition statistics.
License: MIT + file LICENSE
URL: https://github.com/SubhadipJana1409/scCompoundDE
BugReports: https://github.com/SubhadipJana1409/scCompoundDE/issues
biocViews: SingleCell, DifferentialExpression, StatisticalMethod,
        GeneExpression, Transcriptomics, CellBasedAssays, Sequencing,
        WorkflowStep, Transcription
Encoding: UTF-8
Depends: R (>= 4.6.0)
Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors,
        BiocParallel, Matrix, limma, methods, stats, ggplot2, rlang,
        utils
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scuttle,
        withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
git_url: https://git.bioconductor.org/packages/scCompoundDE
git_branch: devel
git_last_commit: baa70ea
git_last_commit_date: 2026-06-30
Repository: Bioconductor 3.24
Date/Publication: 2026-07-07
NeedsCompilation: no
Packaged: 2026-07-08 00:03:50 UTC; biocbuild
Author: Subhadip Jana [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-7860-2853>)
Maintainer: Subhadip Jana <subhadipjana1409@gmail.com>
