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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "scProkaR" in publications use:'
type: software
license: MIT
title: 'scProkaR: Microbial Single-Cell RNA-Seq Analysis for Bacterial Systems'
version: 0.99.2
doi: 10.32614/CRAN.package.scProkaR
abstract: 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.
authors:
- family-names: Zhao
  given-names: Jinxin
  email: jinxin.zhao@monash.edu
  orcid: https://orcid.org/0000-0002-0604-3541
- family-names: Liu
  given-names: Ning
  email: ning.liu@adelaide.edu.au
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/Monash-Li-Lab/scProkaR
commit: 72678d162c6b612cad352f83f5c39cab57b1bb7c
url: https://github.com/Monash-Li-Lab/scProkaR
date-released: '2026-10-11'
contact:
- family-names: Zhao
  given-names: Jinxin
  email: jinxin.zhao@monash.edu
  orcid: https://orcid.org/0000-0002-0604-3541