Package: scBatchQC
Type: Package
Title: Batch-Aware Cell Quality Control for Single-Cell RNA-seq
Version: 0.99.0
Authors@R: c(
    person("Subhadip", "Jana", role = c("aut", "cre"),
           email = "subhadipjana1409@gmail.com",
           comment = c(ORCID = "0009-0003-7860-2853")))
Description: 
    scBatchQC provides a hierarchical empirical Bayes framework for
    quality control in multi-sample, multi-batch single-cell RNA-seq
    experiments. Unlike per-sample QC tools, scBatchQC jointly models
    QC metric distributions (library size, gene count, mitochondrial
    fraction) and doublet rates across batches, enabling calibrated
    cell-level QC calls that account for batch structure. The package
    operates natively on SingleCellExperiment objects and returns
    augmented colData with per-cell QC flags and batch-adjusted doublet
    scores.
License: MIT + file LICENSE
URL: https://github.com/SubhadipJana1409/scBatchQC
BugReports: https://github.com/SubhadipJana1409/scBatchQC/issues
biocViews: SingleCell, QualityControl, BatchEffect, StatisticalMethod,
        Transcriptomics, GeneExpression,CellBasedAssays, Sequencing,
        WorkflowStep
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: SingleCellExperiment, SummarizedExperiment, BiocParallel,
        scuttle, methods, stats, S4Vectors, ggplot2, rlang
Suggests: scDblFinder, BiocStyle, knitr, rmarkdown, testthat (>=
        3.0.0), TENxPBMCData, withr
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-05-04 17:30:46 UTC; pkgbuild
Author: Subhadip Jana [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-7860-2853>)
Maintainer: Subhadip Jana <subhadipjana1409@gmail.com>
