{ "_id": "6acf2440d9de2f3f33fc836a", "Package": "BatchVaria", "Title": "Variance-Aware Evaluation of Batch Correction", "Version": "0.99.2", "Authors@R": "person(\ngiven = \"Nicholas\",\nfamily = \"Moir\",\nemail = \"nicholas.moir@ed.ac.uk\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6957-932X\")\n)", "Description": "Evaluates batch correction in omics data by quantifying\nhow a correction redistributes variance, not only whether it\nremoves it. Records correction and variance-decomposition\nprovenance in the metadata of an ordinary SummarizedExperiment,\nand harmonises both the batch correction methods and the\nvariance-profiling engines behind documented contracts, so that\neither set can be extended without modifying the package.\nVariance fractions are compositional, so removing variance\nassociated with one term inflates the fraction attributed to\nevery other. Each decomposition is therefore recorded alongside\nthe total variance it is relative to and the share an\nunbalanced design cannot attribute to any single term, which is\nwhat distinguishes a correction that removed unwanted variation\nfrom one that merely removed variation.", "License": "Artistic-2.0", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "biocViews": "GeneExpression, RNASeq, BatchEffect, StatisticalMethod,\nSoftware, Normalization, QualityControl, Transcriptomics,\nDataRepresentation, Visualization, Sequencing", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "URL": "https://github.com/cmpmolonc/BatchVaria", "BugReports": "https://github.com/cmpmolonc/BatchVaria/issues", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-15 14:27:22 UTC", "RemoteUrl": "https://github.com/bioc/BatchVaria", "RemoteRef": "HEAD", "RemoteSha": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-14 06:33:27 UTC", "User": "root" }, "Author": "Nicholas Moir [aut, cre] (ORCID:\n)", "Maintainer": "Nicholas Moir ", "_user": "bioc", "_type": "src", "_file": "BatchVaria_0.99.2.tar.gz", "_fileid": "https://r2.ropensci.org/21e44403e7703ef5c14accb0907b785fb360cb4a0f3a10ae68779be594adbc3e", "_filesize": 963152, "_sha256": "21e44403e7703ef5c14accb0907b785fb360cb4a0f3a10ae68779be594adbc3e", "_expires": "2027-01-22T06:42:06.000Z", "_created": "2026-10-14T06:33:27.000Z", "_published": "2026-10-14T06:42:08.414Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_upstream": "https://github.com/bioc/BatchVaria", "_commit": { "id": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "author": "nmoir ", "committer": "nmoir ", "message": "Bump to version 0.99.2.\n\nNEWS records the provenance() and varianceHistory() changes and the\n.check_se() bullet point now matches the requirements page.\n", "time": 1789482442 }, "_maintainer": { "name": "Nicholas Moir", "email": "nicholas.moir@ed.ac.uk", "login": "nmoir", "description": "\n", "uuid": 47523991, "orcid": "0000-0001-6957-932X" }, "_distro": "resolute", "_jobs": [ { "job": 115716663378, "time": 190, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11875340727" }, { "job": 115716663409, "time": 342, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11874806571" }, { "job": 115716663258, "time": 463, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11875276697" }, { "job": 115716663345, "time": 234, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11874406765" }, { "job": 115716663314, "time": 272, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11874511742" }, { "job": 115715209440, "time": 273, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11874760848" }, { "job": 115716663324, "time": 163, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11875046203" }, { "job": 115716663355, "time": 267, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11875291032" }, { "job": 115716663310, "time": 285, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11874292571" }, { "job": 115716663338, "time": 181, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11875120500" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "variancePartition", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "FNN", "role": "Imports" }, { "package": "reformulas", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "limma", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-32", "n": 26 }, { "week": "2026-34", "n": 7 }, { "week": "2026-38", "n": 3 } ], "_tags": [], "_topics": [ "geneexpression", "rnaseq", "batcheffect", "statisticalmethod", "software", "normalization", "qualitycontrol", "transcriptomics", "datarepresentation", "visualization", "sequencing", "batch", "variance" ], "_stars": 0, "_contributors": [ { "user": "nmoir", "count": 43, "uuid": 47523991 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 477, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/cmpmolonc/batchvaria", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/BatchVaria.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "assayVariance", "availableCorrectionMethods", "availableVarianceMethods", "basisProjection", "basisRetention", "compareCorrelations", "comparePCA", "evaluateCorrections", "exampleBatchVaria", "newVarianceSummary", "plotBasisProjection", "plotBatchEntropy", "plotCorrelationChange", "plotPCATrajectory", "plotSampleDistance", "plotVarianceComposition", "plotVarianceDelta", "plotVarianceRadar", "profileVariance", "provenance", "recordVariance", "registerCorrectionMethod", "registerVarianceEngine", "runCorrection", "unregisterCorrectionMethod", "unregisterVarianceEngine", "varianceChange", "varianceDelta", "varianceHistory", "varianceResults", "varianceTable" ], "_help": [ { "page": "assayVariance", "title": "Total variance of each assay", "topics": [ "assayVariance" ] }, { "page": "availableCorrectionMethods", "title": "Available correction methods", "topics": [ "availableCorrectionMethods" ] }, { "page": "availableVarianceMethods", "title": "Available variance profiling methods", "topics": [ "availableVarianceMethods" ] }, { "page": "basisProjection", "title": "Sample coordinates on a reference assay's principal axes", "topics": [ "basisProjection" ] }, { "page": "basisRetention", "title": "Variance retained on a reference assay's principal axes", "topics": [ "basisRetention" ] }, { "page": "BatchVaria-requirements", "title": "Requirements BatchVaria places on a SummarizedExperiment", "topics": [ "BatchVaria-requirements" ] }, { "page": "compareCorrelations", "title": "Compare sample correlation structure across assays", "topics": [ "compareCorrelations" ] }, { "page": "comparePCA", "title": "Compare PCA variance structure across assays", "topics": [ "comparePCA" ] }, { "page": "evaluateCorrections", "title": "Evaluate batch correction performance across assays", "topics": [ "evaluateCorrections" ] }, { "page": "exampleBatchVaria", "title": "Example BatchVaria dataset with batch and biological effects", "topics": [ "exampleBatchVaria" ] }, { "page": "newVarianceSummary", "title": "Build a conforming variance summary", "topics": [ "newVarianceSummary" ] }, { "page": "plotBasisProjection", "title": "Plot samples projected onto a reference assay's basis", "topics": [ "plotBasisProjection" ] }, { "page": "plotBatchEntropy", "title": "Plot batch mixing entropy", "topics": [ "plotBatchEntropy" ] }, { "page": "plotCorrelationChange", "title": "Plot correlation preservation after correction", "topics": [ "plotCorrelationChange" ] }, { "page": "plotPCATrajectory", "title": "Plot PCA correction trajectories", "topics": [ "plotPCATrajectory" ] }, { "page": "plotSampleDistance", "title": "Plot sample distance heatmap", "topics": [ "plotSampleDistance" ] }, { "page": "plotVarianceComposition", "title": "Plot variance composition across model terms", "topics": [ "plotVarianceComposition" ] }, { "page": "plotVarianceDelta", "title": "Plot variance change relative to baseline", "topics": [ "plotVarianceDelta" ] }, { "page": "plotVarianceRadar", "title": "Radar plot of variance redistribution", "topics": [ "plotVarianceRadar" ] }, { "page": "profileVariance", "title": "Profile sources of variance in expression data", "topics": [ "profileVariance" ] }, { "page": "provenance", "title": "Report the analysis history recorded on an object", "topics": [ "provenance" ] }, { "page": "recordVariance", "title": "Record variance decomposition results", "topics": [ "recordVariance" ] }, { "page": "registerCorrectionMethod", "title": "Register a batch correction method", "topics": [ "registerCorrectionMethod" ] }, { "page": "registerVarianceEngine", "title": "Register a variance profiling engine", "topics": [ "registerVarianceEngine" ] }, { "page": "runCorrection", "title": "Apply batch correction to expression data", "topics": [ "runCorrection" ] }, { "page": "unregisterCorrectionMethod", "title": "Remove a registered batch correction method", "topics": [ "unregisterCorrectionMethod" ] }, { "page": "unregisterVarianceEngine", "title": "Remove a registered variance profiling engine", "topics": [ "unregisterVarianceEngine" ] }, { "page": "varianceChange", "title": "Summarise variance change vs raw for a model term", "topics": [ "varianceChange" ] }, { "page": "varianceDelta", "title": "Compute variance redistribution relative to baseline", "topics": [ "varianceDelta" ] }, { "page": "varianceHistory", "title": "Access variance profiling history", "topics": [ "varianceHistory" ] }, { "page": "varianceResults", "title": "Retrieve variance decomposition results", "topics": [ "varianceResults" ] }, { "page": "varianceTable", "title": "Create variance summary tables", "topics": [ "varianceTable" ] } ], "_readme": "https://github.com/bioc/BatchVaria/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "aod", "askpass", "backports", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "broom", "cachem", "caTools", "cli", "codetools", "colorspace", "corpcor", "cowplot", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "Deriv", "doBy", "dplyr", "edgeR", "EnvStats", "fANCOVA", "farver", "fastmap", "FNN", "forecast", "formatR", "fracdiff", "futile.logger", "futile.options", "genefilter", "generics", "GenomicRanges", "ggplot2", "glue", "gplots", "gtable", "gtools", "httr", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "lme4", "lmerTest", "lmtest", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "minqa", "modelr", "mvtnorm", "nlme", "nloptr", "nnet", "nortest", "numDeriv", "openssl", "pbkrtest", "pillar", "pkgconfig", "plyr", "png", "purrr", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "remaCor", "reshape2", "RhpcBLASctl", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sva", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "variancePartition", "vctrs", "viridisLite", "withr", "XML", "xtable", "XVector", "zoo" ], "_vignettes": [ { "source": "BatchVaria-quickstart.Rmd", "filename": "BatchVaria-quickstart.html", "title": "BatchVaria Quickstart: Evaluating Batch Correction Performance", "author": "Nicholas Moir", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installation", "Example Dataset", "Variance Profiling", "What the object is carrying", "Variance Summary Tables", "Variance Composition Table", "Variance Change Relative to Raw", "Total Variance: Reading Fractions Correctly", "Two Engines, One Answer - Until the Design Stops Cooperating", "Interpretation", "Summary Figure", "Diagnostic Plots", "Where the variance sits", "Where the samples sit", "Whether the sample relationships survived", "Whether the batches actually mixed", "Why This Matters", "BatchVaria Workflow Summary", "Summary", "Session Information" ], "created": "2026-08-05 17:38:22", "modified": "2026-08-17 02:50:44", "commits": 7 } ], "_score": 3.1760912590556813, "_indexed": true, "_nocasepkg": "batchvaria", "_universes": [ "bioc", "nmoir", "cmpmolonc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.2", "date": "2026-10-14T06:37:17.000Z", "distro": "resolute", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/39278610851c899d5d1ff93c041001535ece65c2bf9407aaed5d78298575ccb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.6.1", "os": "linux", "version": "0.99.2", "date": "2026-10-14T06:38:39.000Z", "distro": "resolute", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/b8f1d6b6297112bb27830e9dfcaf64bbdc24260b2e95c7f44cb71f45d8c6c27e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.5.3", "os": "mac", "version": "0.99.2", "date": "2026-10-14T06:35:47.000Z", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/a68f93085104c07eaa5657b9751f17743aafdc8f3848220e1426ce70a8069b99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.6.1", "os": "mac", "version": "0.99.2", "date": "2026-10-14T06:35:40.000Z", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/0ef30185953565d11bbc3b6495ef7452bb785431bd8f120db6698fb9ed7e1eb4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.2", "date": "2026-10-14T06:36:39.000Z", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/17b1a279c76293f51b8bd4c4835102eabeff73b4c68436ea954908e6780cd497", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.7.0", "os": "win", "version": "0.99.2", "date": "2026-10-14T06:35:13.000Z", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/946d6c241011d4bb5f9a4ed6dd2bb5f36a29c6c0ae2d838fe87053dfa1bd0a23", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.5.3", "os": "win", "version": "0.99.2", "date": "2026-10-14T06:35:08.000Z", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/51d2ba449b7274d093ae80a847a60b824e3f00602fff2b341678e8d60eecab54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" }, { "r": "4.6.1", "os": "win", "version": "0.99.2", "date": "2026-10-14T06:34:54.000Z", "commit": "c7c8a82e54c13fa0a9557544a8f381e6bcd5eb33", "fileid": "https://r2.ropensci.org/c47da34790fe7517e9b87494b58e1c6c006f0ab4bb90809d785d48823e78211f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38456467920" } ] }