Package: scProkaR
Type: Package
Title: Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems
Version: 0.99.3
Authors@R: 
    c(
        person("Jinxin", "Zhao", email = "jinxin.zhao@monash.edu",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0604-3541")),
        person("Ning", "Liu", email = "ning.liu@adelaide.edu.au",
            role = "aut"),
        person(given = "Alexander von Humboldt Foundation",
            role = "fnd",
            comment = "Fellowship support for Jinxin Zhao")
    )
Description: scProkaR provides a SingleCellExperiment-centred workflow for
    microbial single-cell RNA sequencing data. It standardises bacterial
    input objects from count matrices, 10x Genomics directories or Seurat
    objects, and computes prokaryote-specific quality-control metrics such
    as ribosomal RNA fraction. It performs batch integration with several
    backends and scores the resulting embeddings with scIB-inspired
    benchmarking metrics. It also supports pseudobulk differential
    expression with edgeR and Time Aware Trajectory Analysis (TATA), a
    time-informed trajectory abstraction for perturbation time courses.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-GB
Depends: R (>= 4.6.0)
Imports: bluster, edgeR, ggplot2, grDevices, grid, igraph, Matrix,
        methods, S4Vectors, SingleCellExperiment, splines, stats,
        SummarizedExperiment, utils
Suggests: batchelor, BiocNeighbors, BiocSingular, BiocStyle, cluster,
        DropletUtils, FNN, harmony, irlba, knitr, RANN, rmarkdown,
        scrapper (>= 1.0.0), SeuratObject, testthat (>= 3.0.0), uwot
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Software, SingleCell, RNASeq, Transcriptomics,
        GeneExpression, DifferentialExpression, Clustering,
        GraphAndNetwork, QualityControl, MultipleComparison,
        Normalization, BatchEffect, DimensionReduction, TimeCourse,
        Microbiome, Sequencing, Visualization
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://github.com/Monash-Li-Lab/scProkaR
BugReports: https://github.com/Monash-Li-Lab/scProkaR/issues
git_url: https://git.bioconductor.org/packages/scProkaR
git_branch: devel
git_last_commit: ecce4be
git_last_commit_date: 2026-10-28
Repository: Bioconductor 3.24
Date/Publication: 2026-11-04
NeedsCompilation: no
Packaged: 2026-11-05 01:24:21 UTC; biocbuild
Author: Jinxin Zhao [aut, cre] (ORCID: <https://orcid.org/0000-0002-0604-3541>),
  Ning Liu [aut],
  Alexander von Humboldt Foundation [fnd] (Fellowship support for Jinxin
    Zhao)
Maintainer: Jinxin Zhao <jinxin.zhao@monash.edu>
