{ "_id": "6aad988c3d719c1f84077a6f", "Package": "WithinHostExperiment", "Title": "Within-Host Pathogen Variant QC, Diversity, and Bottleneck", "Version": "0.99.0", "Authors@R": "person(given = \"Cuiwei\", family = \"Gao\",\nemail = \"48gaocuiwei@gmail.com\",\nrole = c(\"aut\", \"cre\"))", "Description": "Provides a SummarizedExperiment-based container and\nworkflow functions for analysing intra-host single nucleotide\nvariants (iSNV) from pathogen deep sequencing data. Supports\nreplicate-aware quality control with full provenance tracking,\nmulti-caller import harmonisation, within-host diversity\nquantification, and standardised export to transmission\nbottleneck estimation tools. Designed as infrastructure that\nbridges upstream variant callers (iVar, LoFreq, Freebayes) with\ndownstream analysis packages through a common data object with\nuncertainty-preserving QC.", "License": "Artistic-2.0", "biocViews": "Genetics, VariantAnnotation, Sequencing, GenomicVariation,\nQualityControl, 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'\n'WithinHostExperiment-package.R' 'adaptive-filter.R'\n'methods.R' 'annotate-gff.R' 'annotate-codon.R' 'bridge.R'\n'bottleneck-exact.R' 'bottleneck-quick.R' 'consensus.R'\n'contamination.R' 'data.R' 'diversity.R' 'import-table.R'\n'import-vcf.R' 'longitudinal.R' 'modeling.R' 'neutrality.R'\n'qc-filters.R' 'qc-replicate.R' 'qc-temporal.R' 'selection.R'\n'sfs.R' 'strand-bias.R' 'validation.R' 'visualization.R'\n'zzz.R'", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-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": { "Date": "2026-09-18 19:51:35 UTC", "User": "root" }, "Author": "Cuiwei Gao [aut, cre]", "Maintainer": "Cuiwei Gao <48gaocuiwei@gmail.com>", "_user": "biocstaging", "_type": "src", "_file": "WithinHostExperiment_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/a9c2cbcc4ca676d90c3bb57883d2df27f357dae56a08bf66267a03f41cb76aaa", "_filesize": 1020084, "_sha256": "a9c2cbcc4ca676d90c3bb57883d2df27f357dae56a08bf66267a03f41cb76aaa", "_expires": "2026-12-27T20:01:13.000Z", "_created": "2026-09-18T19:51:35.000Z", "_published": "2026-09-18T20:01:16.765Z", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387818608", "_status": "success", "_upstream": "https://github.com/BiocStaging/WithinHostExperiment", "_commit": { "id": "28a1a5c5a77399ceaa85502f2893d28071b1457e", "author": "CuiweiG <48gaocuiwei@gmail.com>", "committer": "CuiweiG <48gaocuiwei@gmail.com>", "message": "docs: make the vignette's prose agree with its own output\n\nAfter the cross-pathogen neutrality table the vignette said negative\nTajima's D and Fu's Fs \"are expected for within-host pathogen\npopulations\". The table printed just above shows D of +2.37 for\ninfluenza and +2.12 for HIV-1. The fixtures are synthetic and the\ntuberculosis one has three sites, so the text now says the signs carry\nno biological meaning here and what each sign is usually taken to mean\nin real data. The column that counted rows is named n_sites rather\nthan S, since it counts every site in the object, not segregating\nsites passing QC.\n\nThe case study called household HH6 \"an epidemiologically confirmed\ndonor-recipient pair\". The study's pair table lists the household in\nboth directions, as HH6_A and HH6_B, so direction is not established;\nthe text says so and that the example follows HH6_A for illustration.\n\nThe QC section printed an audit log with 39 cells passed, a per-sample\nsummary with 24 calls passed, and a filter demonstration that kept 20\nof 20 sites straight after a site was flagged. All three are correct,\nbut nothing explained them. A paragraph now says that qcLog() counts\nsite-by-sample cells including absent calls, that qcSummary() counts\ncalls, and that passedISNV() keeps a site any sample passes.\n\nThe reporting chunk added in the previous round had each \"\\n\" escape\nexpanded into a real newline inside its string literals, so the\ndisplayed code showed a lone closing quote on the following line. The\nescapes are restored. The pipe example no longer prints forty lines of\npackage start-up messages, and the three figures have captions, given\nas #| options so no chunk header exceeds 80 characters.\n", "time": 1789603983 }, "_maintainer": { "name": "Cuiwei Gao", "email": "48gaocuiwei@gmail.com", "login": "cuiweig", "mastodon": "@cuiweigao@mastodon.social", "twitter": "@CuiweiG23", "description": "R package developer · Biostatistics · Mechanical engineering · Data analysis", "uuid": 199837382 }, "_distro": "resolute", "_jobs": [ { "job": 105740540963, "time": 205, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "10564279521" }, { "job": 105740541171, "time": 411, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10564703948" }, { "job": 105740540921, "time": 401, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10565205179" }, { "job": 105740540999, "time": 248, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": 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}, { "page": "estimateSelectionCoefficient", "title": "Estimate selection coefficient from frequency trajectory", "topics": [ "estimateSelectionCoefficient" ] }, { "page": "exactBottleneck", "title": "Exact bottleneck size estimation", "topics": [ "exactBottleneck" ] }, { "page": "example_whe", "title": "Example WithinHostExperiment dataset", "topics": [ "example_whe" ] }, { "page": "exportPairFrequencies", "title": "Export donor-recipient frequency table", "topics": [ "exportPairFrequencies" ] }, { "page": "fitDiversityModel", "title": "Fit a linear model to diversity data", "topics": [ "fitDiversityModel" ] }, { "page": "flagISNV", "title": "Flag iSNV sites based on quality criteria", "topics": [ "flagISNV", "flagISNV,WithinHostExperiment-method" ] }, { "page": "flagPrimerSites", "title": "Flag iSNVs in primer binding regions", "topics": [ "flagPrimerSites" ] }, { "page": "flagReplicateDiscordance", "title": "Flag iSNVs with replicate discordance", "topics": [ "flagReplicateDiscordance" ] }, { "page": "flagStrandBiasSCI", "title": "Flag strand-biased iSNVs using the SCI metric", "topics": [ "flagStrandBiasSCI" ] }, { "page": "flagTemporalInconsistency", "title": "Flag temporally inconsistent iSNVs in longitudinal data", "topics": [ "flagTemporalInconsistency" ] }, { "page": "fusFs", "title": "Fu's Fs statistic", "topics": [ "fusFs" ] }, { "page": "ISNVFilter", "title": "Create an ISNVFilter object", "topics": [ "ISNVFilter" ] }, { "page": "ISNVFilter-class", "title": "ISNVFilter: Quality control filter for iSNV analysis", "topics": [ ".ISNVFilter", "ISNVFilter-class", "show,ISNVFilter-method" ] }, { "page": "multitestCorrection", "title": "Multiple testing correction for p-values", "topics": [ "multitestCorrection" ] }, { "page": "neutralityFromSFS", "title": "Compute all neutrality statistics from a WithinHostSFS", "topics": [ "neutralityFromSFS" ] }, { "page": "permutationTest", "title": "Permutation test for two-group comparison", "topics": [ "permutationTest" ] }, { "page": "piISNV", "title": "Nucleotide diversity (pi) from iSNV frequencies", "topics": [ "piISNV" ] }, { "page": "plotFrequencySpectrum", "title": "Plot iSNV frequency spectrum", "topics": [ "plotFrequencySpectrum" ] }, { "page": "plotFrequencyTrajectory", "title": "Plot allele frequency trajectories over time", "topics": [ "plotFrequencyTrajectory" ] }, { "page": "plotPairScatter", "title": "Plot donor-recipient frequency scatter", "topics": [ "plotPairScatter" ] }, { "page": "plotQCDashboard", "title": "QC dashboard plot", "topics": [ "plotQCDashboard" ] }, { "page": "plotSFS", "title": "Plot a within-host site frequency spectrum", "topics": [ "plotSFS" ] }, { "page": "WHE-accessors", "title": "Access the QC audit log", "topics": [ "passedISNV", "passedISNV,WithinHostExperiment-method", "qcFilters", "qcFilters,WithinHostExperiment-method", "qcFilters<-", "qcFilters<-,WithinHostExperiment-method", "qcLog", "qcLog,WithinHostExperiment-method", 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"page": "trackFrequency", "title": "Track variant frequency trajectories over time", "topics": [ "trackFrequency" ] }, { "page": "validateDiversity", "title": "Check diversity estimates against plausibility ranges", "topics": [ "validateDiversity" ] }, { "page": "wattersonISNV", "title": "Watterson's theta from iSNV count", "topics": [ "wattersonISNV" ] }, { "page": "WHE-combine", "title": "Combine WithinHostExperiment objects by rows or columns", "topics": [ "combineCols,WithinHostExperiment-method", "combineRows,WithinHostExperiment-method", "WHE-combine" ] }, { "page": "WithinHostExperiment", "title": "Create a WithinHostExperiment from components", "topics": [ "WithinHostExperiment" ] }, { "page": "WithinHostExperiment-class", "title": "WithinHostExperiment: Container for within-host pathogen variant data", "topics": [ ".WithinHostExperiment", "show,WithinHostExperiment-method", "WithinHostExperiment-class", "[,WithinHostExperiment,ANY,ANY,ANY-method" ] }, { "page": 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