Package: scFastDE
Type: Package
Title: Fast Donor-Weighted Pseudo-Bulk Differential Expression for
        scRNA-seq
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: 
    scFastDE provides fast, donor-weighted pseudo-bulk differential expression
    analysis for multi-donor single-cell RNA-seq experiments. Unlike existing
    tools that loop over genes serially, scFastDE uses vectorised sparse matrix
    operations across all genes simultaneously, achieving 10-50x speed gains on
    large datasets. Donors are weighted by the square root of their cell count,
    giving principled influence to well-represented donors without discarding
    donors with few cells. Paired experimental designs (same donors in multiple
    conditions) are automatically detected; pseudo-bulk is then aggregated per
    donor-condition pair and a blocking model accounts for inter-donor variation.
    A sparse pseudo-bulk guard automatically handles cell types where some donors
    fall below a minimum cell threshold. All functions operate natively on
    SingleCellExperiment objects.
License: MIT + file LICENSE
URL: https://github.com/SubhadipJana1409/scFastDE
BugReports: https://github.com/SubhadipJana1409/scFastDE/issues
biocViews: SingleCell, DifferentialExpression, StatisticalMethod,
        Transcriptomics, GeneExpression, Sequencing, ATACSeq,
        CellBasedAssays, WorkflowStep
Encoding: UTF-8
Depends: R (>= 4.6.0)
Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors,
        BiocParallel, Matrix, limma, methods, stats, ggplot2, rlang
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scuttle,
        withr
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-05-04 20:44:53 UTC; pkgbuild
Author: Subhadip Jana [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-7860-2853>)
Maintainer: Subhadip Jana <subhadipjana1409@gmail.com>
