This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see BatchQC.

Batch Effects Quality Control Software

Bioconductor version: 3.18

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.

Author: Solaiappan Manimaran <manimaran_1975 at>, W. Evan Johnson <wej at>, Heather Selby <selbyh at>, Claire Ruberman <claireruberman at>, Kwame Okrah <kwame.okrah at>, Hector Corrada Bravo <hcorrada at>

Maintainer: Solaiappan Manimaran <manimaran_1975 at>

Citation (from within R, enter citation("BatchQC")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

BatchQC_examples HTML
BatchQC_usage_advanced PDF R Script
BatchQCIntro HTML
Reference Manual PDF


biocViews BatchEffect, DifferentialExpression, GraphAndNetwork, ImmunoOncology, Microarray, Preprocessing, PrincipalComponent, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva, corpcor, moments, matrixStats, ggvis, heatmaply, reshape2, limma, grDevices, graphics, stats, methods, Matrix
System Requirements pandoc ( for generating reports from markdown files.
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Follow Installation instructions to use this package in your R session.

Source Package BatchQC_1.30.0.tar.gz
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macOS Binary (x86_64) BatchQC_1.30.0.tgz
macOS Binary (arm64) BatchQC_1.30.0.tgz
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