Type: Package
Package: BatchQC
Title: Batch Effects Quality Control Software
Version: 2.9.0
Date: 2026-02-10
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: Sequencing and microarray samples 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, GeneExpression, GraphAndNetwork, Microarray,
        Normalization, PrincipalComponent, Sequencing, Software,
        Visualization, QualityControl, RNASeq, Preprocessing,
        DifferentialExpression, ImmunoOncology
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
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/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: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:43:18 UTC
RemoteUrl: https://github.com/bioc/BatchQC
RemoteRef: HEAD
RemoteSha: c30deb77cff40579d766f9cae59b0c94fd07dd86
NeedsCompilation: no
Packaged: 2026-06-10 07:02:23 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>