Package: scFastDE
Type: Package
Title: Fast Donor-Weighted Pseudo-Bulk Differential Expression for
        scRNA-seq
Version: 0.99.3
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 (>= 4.5.0)
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: 2026-06-04 09:20:04 UTC
RemoteUrl: https://github.com/bioc/scFastDE
RemoteRef: HEAD
RemoteSha: 543071ed85a3d260095cf95942c55c4df5d8fcc8
NeedsCompilation: no
Packaged: 2026-06-28 11:12:41 UTC; root
Author: Subhadip Jana [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-7860-2853>)
Maintainer: Subhadip Jana <subhadipjana1409@gmail.com>