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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 "WithinHostExperiment" in publications use:'
type: software
license: Artistic-2.0
title: 'WithinHostExperiment: Within-Host Pathogen Variant QC, Diversity, and Bottleneck'
version: 0.99.0
abstract: Provides a SummarizedExperiment-based container and workflow functions for
  analysing intra-host single nucleotide variants (iSNV) from pathogen deep sequencing
  data. Supports replicate-aware quality control with full provenance tracking, multi-caller
  import harmonisation, within-host diversity quantification, and standardised export
  to transmission bottleneck estimation tools. Designed as infrastructure that bridges
  upstream variant callers (iVar, LoFreq, Freebayes) with downstream analysis packages
  through a common data object with uncertainty-preserving QC.
authors:
- family-names: Gao
  given-names: Cuiwei
  email: 48gaocuiwei@gmail.com
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/CuiweiG/WithinHostExperiment
commit: 28a1a5c5a77399ceaa85502f2893d28071b1457e
url: https://github.com/CuiweiG/WithinHostExperiment
date-released: '2026-09-17'
contact:
- family-names: Gao
  given-names: Cuiwei
  email: 48gaocuiwei@gmail.com