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 (>= 4.6.0), 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
git_url: https://git.bioconductor.org/packages/BatchVaria
git_branch: devel
git_last_commit: c7c8a82
git_last_commit_date: 2026-09-15
Repository: Bioconductor 3.24
Date/Publication: 2026-10-13
NeedsCompilation: no
Packaged: 2026-10-13 20:26:42 UTC; biocbuild
Author: Nicholas Moir [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6957-932X>)
Maintainer: Nicholas Moir <nicholas.moir@ed.ac.uk>
