Package: BatchVaria
Title: Variance-Aware Evaluation of Batch Correction
Version: 0.99.2
Authors@R: 
    person(
        given = "Nicholas",
        family = "Moir",
        email = "nicholas.moir@ed.ac.uk",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0001-6957-932X")
    )
Description: Evaluates batch correction in omics data by quantifying
        how a correction redistributes variance, not only whether it
        removes it. Records correction and variance-decomposition
        provenance in the metadata of an ordinary SummarizedExperiment,
        and harmonises both the batch correction methods and the
        variance-profiling engines behind documented contracts, so that
        either set can be extended without modifying the package.
        Variance fractions are compositional, so removing variance
        associated with one term inflates the fraction attributed to
        every other. Each decomposition is therefore recorded alongside
        the total variance it is relative to and the share an
        unbalanced design cannot attribute to any single term, which is
        what distinguishes a correction that removed unwanted variation
        from one that merely removed variation.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.5.0), SummarizedExperiment
Roxygen: list(markdown = TRUE)
biocViews: GeneExpression, RNASeq, BatchEffect, StatisticalMethod,
        Software, Normalization, QualityControl, Transcriptomics,
        DataRepresentation, Visualization, Sequencing
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, limma
VignetteBuilder: knitr
Imports: S4Vectors, rlang, methods, variancePartition, stats, ggplot2,
        FNN, reformulas, sva, tidyr, tidyselect, dplyr, grid
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
        libssl-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: 2026-10-14 06:33:27 UTC; root
Author: Nicholas Moir [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6957-932X>)
Maintainer: Nicholas Moir <nicholas.moir@ed.ac.uk>