Package: WithinHostExperiment
Title: Within-Host Pathogen Variant QC, Diversity, and Bottleneck
Version: 0.99.0
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 (>= 4.5.0)
Imports: methods, BiocGenerics, S4Vectors (>= 0.32.0), IRanges,
        GenomicRanges, SummarizedExperiment, GenomeInfoDb,
        VariantAnnotation, stats, utils
Suggests: ggplot2 (>= 3.4.0), patchwork, testthat (>= 3.1.5), knitr,
        rmarkdown, BiocCheck, covr
biocViews: Genetics, VariantAnnotation, Sequencing, GenomicVariation,
        QualityControl, VariantDetection, DataImport, LongRead
URL: https://github.com/CuiweiG/WithinHostExperiment
BugReports: https://github.com/CuiweiG/WithinHostExperiment/issues
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/testthat/edition: 3
Collate: 'AllClasses.R' 'AllGenerics.R'
        'WithinHostExperiment-package.R' 'adaptive-filter.R'
        'methods.R' 'annotate-gff.R' 'annotate-codon.R' 'bridge.R'
        'bottleneck-exact.R' 'bottleneck-quick.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'
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-17 00:13:03 UTC
RemoteUrl: https://github.com/BiocStaging/WithinHostExperiment
RemoteRef: HEAD
RemoteSha: 28a1a5c5a77399ceaa85502f2893d28071b1457e
NeedsCompilation: no
Packaged: 2026-09-18 19:51:35 UTC; root
Author: Cuiwei Gao [aut, cre]
Maintainer: Cuiwei Gao <48gaocuiwei@gmail.com>