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 (>= 4.5.0)
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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-30 10:15:57 UTC
RemoteUrl: https://github.com/bioc/scCompoundDE
RemoteRef: HEAD
RemoteSha: baa70eacf60c62657a90813dc621c0f63a1449c6
NeedsCompilation: no
Packaged: 2026-07-09 17:16:15 UTC; root
Author: Subhadip Jana [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-7860-2853>)
Maintainer: Subhadip Jana <subhadipjana1409@gmail.com>
Built: R 4.6.1; ; 2026-07-09 17:19:05 UTC; unix
