Type: Package
Package: BatchQC
Title: Batch Effects Quality Control Software
Version: 2.8.3
Date: 2026-08-28
Authors@R: c(
    person("Jessica", "Anderson", , "anderson.jessica@rutgers.edu", 
    role = c("aut"), comment = c(ORCID = "0000-0002-0542-9872")),
    person("W. Evan", "Johnson", , "wj183@njms.rutgers.edu",
    role = c("aut", "fnd"), comment = c(ORCID = "0000-0002-6247-6595")),
    person("Yaoan", "Leng", , "leng@bu.edu", role = c("ctb", "cre"),
    comment = c(ORCID = "0009-0002-3957-5250")),
    person("Solaiappan", "Manimaran", , "manimaran_1975@hotmail.com", role = "aut"),
    person("Heather", "Selby", , "selbyh@bu.edu", role = "ctb"),
    person("Claire", "Ruberman", , "claireruberman@gmail.com", role = "ctb"),
    person("Kwame", "Okrah", , "kwame.okrah@gmail.com", role = "ctb"),
    person("Hector Corrada", "Bravo", , "hcorrada@gmail.com", role = "ctb"),
    person("Michael", "Silverstein", , "msilver4@bu.edu", role = "ctb"),
    person("Regan", "Conrad", , "rdconrad@bu.edu", role = "ctb"),
    person("Zhaorong", "Li", , "zhaorong@bu.edu", role = "ctb"),
    person("Evan", "Holmes", , "evanjh19@gmail.com", role = "ctb"),
    person("Solomon", "Joseph", , "sj1136@njms.rutgers.edu", role = "ctb"),
    person("Howard", "Fan", , "hf268@njms.rutgers.edu", role = "ctb"),
    person("Sean", "Lu", , "sl1729@njms.rutgers.edu", role = "ctb")
  )
Description: Samples (-omics, imaging, single cell, etc) often are
        collected or processed in multiple batches or at different
        times. This often produces technical biases that can lead to
        incorrect results in the downstream analysis. BatchQC is a
        software tool that streamlines batch preprocessing and
        evaluation by providing interactive diagnostics,
        visualizations, and statistical analyses to explore the extent
        to which batch variation impacts the data. BatchQC diagnostics
        help determine whether batch adjustment needs to be done, and
        how correction should be applied before proceeding with a
        downstream analysis. Moreover, BatchQC interactively applies
        multiple common batch effect approaches to the data and the
        user can quickly see the benefits of each method. BatchQC is
        developed as a Shiny App. The output is organized into multiple
        tabs and each tab features an important part of the batch
        effect analysis and visualization of the data. The BatchQC
        interface has the following analysis groups: Summary,
        Differential Expression, Median Correlations, Heatmaps,
        Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.
License: MIT + file LICENSE
URL: https://github.com/wejlab/BatchQC
BugReports: https://github.com/wejlab/BatchQC/issues
Depends: R (>= 4.5.0)
Imports: data.table, DESeq2, dplyr, EBSeq, edgeR, FNN, ggdendro,
        ggnewscale, ggplot2, ggpubr, Harman, limma, matrixStats,
        methods, MASS, pheatmap, RColorBrewer, reader, reshape2, scran,
        shiny, shinyjs, shinythemes, stats, SummarizedExperiment, sva,
        S4Vectors, tibble, tidyr, tidyverse, umap, utils
Suggests: BiocManager, BiocStyle, bladderbatch, curatedTBData,
        devtools, knitr, lintr, MultiAssayExperiment, plotly,
        rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: BatchEffect, DifferentialExpression, GeneExpression,
        GraphAndNetwork, ImmunoOncology, Microarray, Normalization,
        Preprocessing, PrincipalComponent, QualityControl, RNASeq,
        Sequencing, ShinyApps, Software, Visualization
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
Collate: 'Normalization.R' 'batch_correction.R' 'color_palette.R'
        'compute_aic.R' 'covariates_not_confounded.R' 'data.R'
        'dendrogram.R' 'dendrogram_alpha_numeric_check.R'
        'dendrogram_color_palette.R' 'differential_expression.R'
        'explained_variation.R' 'global_vars.R' 'heatmap.R'
        'heatmap_num_to_char_convertor.R' 'import.R' 'kBET-utils.R'
        'kBET.R' 'lambda_statistic.R' 'negative_binomial_check.R'
        'pca.R' 'preprocess.R' 'runApp.R' 'summary_statistics.R'
        'umap.R' 'variation_ratios.R' 'volcano_plot.R'
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev
        libxml2-dev libssl-dev python3 libx11-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-09-14 19:54:49 UTC
RemoteUrl: https://github.com/bioc/BatchQC
RemoteRef: RELEASE_3_23
RemoteSha: 9daabc96fa6b48fda3354cf80bb0991ab227512a
NeedsCompilation: no
Packaged: 2026-10-14 11:33:37 UTC; root
Author: Jessica Anderson [aut] (ORCID: <https://orcid.org/0000-0002-0542-9872>),
  W. Evan Johnson [aut, fnd] (ORCID:
    <https://orcid.org/0000-0002-6247-6595>),
  Yaoan Leng [ctb, cre] (ORCID: <https://orcid.org/0009-0002-3957-5250>),
  Solaiappan Manimaran [aut],
  Heather Selby [ctb],
  Claire Ruberman [ctb],
  Kwame Okrah [ctb],
  Hector Corrada Bravo [ctb],
  Michael Silverstein [ctb],
  Regan Conrad [ctb],
  Zhaorong Li [ctb],
  Evan Holmes [ctb],
  Solomon Joseph [ctb],
  Howard Fan [ctb],
  Sean Lu [ctb]
Maintainer: Yaoan Leng <leng@bu.edu>