Package: WithinHostExperiment
Title: Within-Host Pathogen Variant QC, Diversity, and Bottleneck
Version: 0.99.2
Authors@R: 
    person(given = "Cuiwei", family = "Gao",
    email = "48gaocuiwei@gmail.com",
    role = c("aut", "cre"))
Description: 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.
License: Artistic-2.0
Depends: R (>= 4.6.0)
Imports: methods, BiocGenerics, S4Vectors (>= 0.32.0), IRanges,
        GenomicRanges, SummarizedExperiment, GenomeInfoDb, Biostrings,
        GenomicFeatures, VariantAnnotation, graphics, stats, tools,
        utils
Suggests: BiocStyle, ggplot2 (>= 3.4.0), patchwork, testthat (>=
        3.1.5), knitr, rmarkdown, BiocCheck, rtracklayer, txdbmaker,
        MSA2dist
biocViews: Genetics, VariantAnnotation, Sequencing, GenomicVariation,
        QualityControl, VariantDetection, DataImport
URL: https://github.com/CuiweiG/WithinHostExperiment
BugReports: https://github.com/CuiweiG/WithinHostExperiment/issues
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
Config/testthat/edition: 3
Collate: 'AllClasses.R' 'AllGenerics.R'
        'WithinHostExperiment-package.R' 'adaptive-filter.R'
        'methods.R' 'annotate-genes.R' 'annotate-codon.R' 'bridge.R'
        'bottleneck-exact.R' 'bottleneck-quick.R'
        'consensus-sequences.R' 'consensus.R' 'contamination.R'
        'data.R' 'diversity.R' 'import-table.R' 'import-vcf.R'
        'longitudinal.R' 'modeling.R' 'neutrality.R' 'qc-filters.R'
        'qc-replicate.R' 'qc-temporal.R' 'selection.R' 'sfs.R'
        'strand-bias.R' 'validation.R' 'visualization.R' 'zzz.R'
RoxygenNote: 7.3.3
git_url: https://git.bioconductor.org/packages/WithinHostExperiment
git_branch: devel
git_last_commit: 89c27e8
git_last_commit_date: 2026-10-25
Repository: Bioconductor 3.24
Date/Publication: 2026-10-29
NeedsCompilation: no
Packaged: 2026-10-30 01:59:49 UTC; biocbuild
Author: Cuiwei Gao [aut, cre]
Maintainer: Cuiwei Gao <48gaocuiwei@gmail.com>
