{ "_id": "6ae38fc48d250e7ad09f0d35", "Package": "WithinHostExperiment", "Title": "Within-Host Pathogen Variant QC, Diversity, and Bottleneck", "Version": "0.99.2", "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", "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'\n'WithinHostExperiment-package.R' 'adaptive-filter.R'\n'methods.R' 'annotate-genes.R' 'annotate-codon.R' 'bridge.R'\n'bottleneck-exact.R' 'bottleneck-quick.R'\n'consensus-sequences.R' 'consensus.R' 'contamination.R'\n'data.R' 'diversity.R' 'import-table.R' 'import-vcf.R'\n'longitudinal.R' 'modeling.R' 'neutrality.R' 'qc-filters.R'\n'qc-replicate.R' 'qc-temporal.R' 'selection.R' 'sfs.R'\n'strand-bias.R' 'validation.R' 'visualization.R' 'zzz.R'", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-25 07:53:43 UTC", "RemoteUrl": "https://github.com/bioc/WithinHostExperiment", "RemoteRef": "HEAD", "RemoteSha": "89c27e8b31fd07dd93a0c81ab94d5a5bb77c52bf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 17:53:28 UTC", "User": "root" }, "Author": "Cuiwei Gao [aut, cre]", "Maintainer": "Cuiwei Gao <48gaocuiwei@gmail.com>", "_user": "bioc", "_type": "src", "_file": "WithinHostExperiment_0.99.2.tar.gz", "_fileid": "https://r2.ropensci.org/5d694141b08fadf2316f5dca34be770d9bb60b669a31e935ecfa5bc215729cc5", "_filesize": 1442836, "_sha256": "5d694141b08fadf2316f5dca34be770d9bb60b669a31e935ecfa5bc215729cc5", "_expires": "2027-02-06T18:26:09.000Z", "_created": "2026-10-29T17:53:28.000Z", "_published": "2026-10-29T18:26:12.820Z", "_upstream": "https://github.com/bioc/WithinHostExperiment", "_status": "success", "_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 }, "_jobs": [ { "job": 123630806395, "time": 200, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12920850904" }, { "job": 123630806479, "time": 472, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12921720207" }, { "job": 123630806496, "time": 552, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12921091272" }, { "job": 123630806423, "time": 605, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12921798369" }, { "job": 123630806586, "time": 546, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12921834185" }, { "job": 123625611667, "time": 563, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12921225009" }, { "job": 123630806554, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12920217408" }, { "job": 123630806664, "time": 515, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12920587237" }, { "job": 123630806593, "time": 508, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12921096729" }, { "job": 123630806552, "time": 500, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12921101579" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40924267977", "_commit": { "id": "89c27e8b31fd07dd93a0c81ab94d5a5bb77c52bf", "author": "CuiweiG <48gaocuiwei@gmail.com>", "committer": "CuiweiG <48gaocuiwei@gmail.com>", "message": "Say which correctSFSBias() method the NEWS example figures are for\n\nThe 0.99.2 entry said the help page's example kept its 15 sites and now\nhas 16. That is the truncation method; the example itself runs the\nbinomial method, which gives 15 before and after because every bin is\ndetectable at its median depth of 1,600 reads. 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Diversity, and Bottleneck", "topics": [ "WithinHostExperiment-package" ] }, { "page": "adaptiveFilter", "title": "Create a technology-appropriate ISNVFilter", "topics": [ "adaptiveFilter" ] }, { "page": "annotateCodonChange", "title": "Codon and amino acid consequence of each SNV", "topics": [ "annotateCodonChange", "annotateCodonChange,WithinHostExperiment,ANY,character-method", "annotateCodonChange,WithinHostExperiment,ANY,XString-method", "annotateCodonChange,WithinHostExperiment,character,DNAStringSet-method", "annotateCodonChange,WithinHostExperiment,GRanges,DNAStringSet-method", "annotateCodonChange,WithinHostExperiment,GRangesList,DNAStringSet-method", "annotateCodonChange,WithinHostExperiment,TxDb,DNAStringSet-method" ] }, { "page": "annotateGenes", "title": "Label variant sites with the genes they overlap", "topics": [ "annotateGenes", "annotateGenes,WithinHostExperiment,GRanges-method", "annotateGenes,WithinHostExperiment,TxDb-method" ] }, { "page": "asViralBottleneckInput", "title": "Export data for ViralBottleneck package", "topics": [ "asViralBottleneckInput" ] }, { "page": "benchmarkCallers", "title": "Benchmark variant callers against truth or each other", "topics": [ "benchmarkCallers" ] }, { "page": "buildSFS", "title": "Build a site frequency spectrum from a WithinHostExperiment", "topics": [ "buildSFS" ] }, { "page": "buildSFSList", "title": "Build SFS for all samples in a WithinHostExperiment", "topics": [ "buildSFSList" ] }, { "page": "calcCallerConcordance", "title": "Pairwise caller concordance matrix", "topics": [ "calcCallerConcordance" ] }, { "page": "calcDiversity", "title": "Compute within-host diversity indices", "topics": [ "calcDiversity", "calcDiversity,WithinHostExperiment-method" ] }, { "page": "calcNeutralityTests", "title": "Compute neutrality test statistics", "topics": [ "calcNeutralityTests", "calcNeutralityTests,WithinHostExperiment-method" ] }, { "page": "calcSharedVariants", "title": "Calculate shared variant statistics", "topics": [ "calcSharedVariants" ] }, { "page": "chao1ISNV", "title": "Chao1 richness estimator for iSNV data", "topics": [ "chao1ISNV" ] }, { "page": "checkDiversityPlausibility", "title": "Check diversity estimates against heuristic plausibility ranges", "topics": [ "checkDiversityPlausibility" ] }, { "page": "coerce-WHE", "title": "Convert between WithinHostExperiment, data.frame, VRanges and VCF", "topics": [ "coerce,VCF,WithinHostExperiment-method", "coerce,VRanges,WithinHostExperiment-method", "coerce,WithinHostExperiment,data.frame-method", "coerce,WithinHostExperiment,VRanges-method", "coerce-WHE" ] }, { "page": "compareDiversity", "title": "Compare diversity between sample groups", "topics": [ "compareDiversity" ] }, { "page": "compareSFS", "title": "Compare two within-host SFS objects", "topics": [ "compareSFS" ] }, { "page": "ConcordanceRule", "title": "Create a ConcordanceRule object", "topics": [ "ConcordanceRule" ] }, { "page": "ConcordanceRule-class", "title": "ConcordanceRule: agreement required between technical replicates", "topics": [ ".ConcordanceRule", "ConcordanceRule-class", "show,ConcordanceRule-method" ] }, { "page": "consensusISNV", "title": "Multi-caller consensus iSNV detection", "topics": [ "consensusISNV" ] }, { "page": "consensusSequences", "title": "Consensus sequence of each sample", "topics": [ "consensusSequences", "consensusSequences,WithinHostExperiment,character-method", "consensusSequences,WithinHostExperiment,DNAStringSet-method", "consensusSequences,WithinHostExperiment,XString-method" ] }, { "page": "correctSFSBias", "title": "Correct ascertainment bias in the within-host SFS", "topics": [ "correctSFSBias" ] }, { "page": "detectCrossContamination", "title": "Detect potential cross-contamination between samples", "topics": [ "detectCrossContamination" ] }, { "page": "detectEmergingVariants", "title": "Detect emerging variants across time points", "topics": [ "detectEmergingVariants" ] }, { "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": "pNpSWithinHost", "title": "Within-host pN/pS ratio", "topics": [ "pNpSWithinHost", "pNpSWithinHost,WithinHostExperiment,ANY,character-method", "pNpSWithinHost,WithinHostExperiment,ANY,XString-method", "pNpSWithinHost,WithinHostExperiment,character,DNAStringSet-method", 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"Import iSNV data from tabular files", "topics": [ "readWithinHostTable" ] }, { "page": "sciStrandBias", "title": "Strand Coverage Imbalance (SCI) score", "topics": [ "sciStrandBias" ] }, { "page": "shannonISNV", "title": "Shannon entropy from iSNV frequencies", "topics": [ "shannonISNV" ] }, { "page": "simpsonISNV", "title": "Simpson diversity index for iSNV frequencies", "topics": [ "simpsonISNV" ] }, { "page": "tajimaD", "title": "Tajima's D statistic", "topics": [ "tajimaD" ] }, { "page": "trackFrequency", "title": "Track variant frequency trajectories over time", "topics": [ "trackFrequency" ] }, { "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": "WithinHostSFS-class", "title": "WithinHostSFS: Site Frequency Spectrum for within-host variants", "topics": [ ".WithinHostSFS", "show,WithinHostSFS-method", "WithinHostSFS", "WithinHostSFS-class" ] } ], "_readme": "https://github.com/bioc/WithinHostExperiment/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", 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table", "The first added slot: qcLog", "The second added slot: qcFilters", "What subsetting and combining do to the two slots", "What the validity method enforces", "Converting to other containers", "Importing calls", "From VCF files", "From a VCF already read into R", "From an iVar table", "Quality control", "Describing a filter", "Applying a filter", "Summarising quality per sample", "Extracting the calls that passed", "Technology-specific defaults", "Replicate-aware quality control", "Masking primer sites", "Strand bias", "Detecting cross-contamination", "Putting the steps together", "Annotation", "Labelling sites with genes", "Codon and amino acid consequences", "Diversity", "How much variation a host carries", "Checking an estimate for plausibility", "Modelling diversity across samples", "Site frequency spectrum", "Building a spectrum", "Correcting for what could not be seen", "Comparing two spectra", "Neutrality and selection", "Neutrality statistics from the object", "Statistics from a spectrum, including Fay and Wu's H", "Within-host pN/pS", "Consensus sequences for between-host comparison", "Selection coefficients from a trajectory", "Transmission", "Finding the pairs", "Counting shared variants", "A quick bottleneck estimate", "Estimators that model depth", "Exporting for other tools", "Longitudinal data", "Tracking frequencies over time", "Detecting emerging variants", "Flagging temporally inconsistent sites", "Several callers", "Building a consensus call set", "Measuring agreement between callers", "Statistics", "Visualisation", "The frequency spectrum of an object", "Donor against recipient", "A quality-control dashboard", "A spectrum object", "A trajectory", "A worked example on real data", "The data", "Recording the genome length", "Quality control and diversity", "Checking the magnitudes", "Other pathogens", "Influenza A", "HIV-1", "Mycobacterium tuberculosis", "Neutrality statistics across the three", "Scope and limitations", "Glossary", 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