Package: scProkaR
Type: Package
Title: Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems
Version: 0.99.2
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")
    )
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 (>= 4.5.0)
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
Config/pak/sysreqs: libglpk-dev libxml2-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-11 19:52:50 UTC
RemoteUrl: https://github.com/BiocStaging/scProkaR
RemoteRef: HEAD
RemoteSha: 72678d162c6b612cad352f83f5c39cab57b1bb7c
NeedsCompilation: no
Packaged: 2026-10-11 20:30:38 UTC; root
Author: Jinxin Zhao [aut, cre] (ORCID: <https://orcid.org/0000-0002-0604-3541>),
  Ning Liu [aut]
Maintainer: Jinxin Zhao <jinxin.zhao@monash.edu>