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BatchQC

Batch Effects Quality Control Software


Bioconductor version: Release (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 hotmail.com>, W. Evan Johnson <wej at bu.edu>, Heather Selby <selbyh at bu.edu>, Claire Ruberman <claireruberman at gmail.com>, Kwame Okrah <kwame.okrah at gmail.com>, Hector Corrada Bravo <hcorrada at gmail.com>

Maintainer: Solaiappan Manimaran <manimaran_1975 at hotmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BatchQC")

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

Documentation

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

browseVignettes("BatchQC")
BatchQC_examples HTML
BatchQC_usage_advanced PDF R Script
BatchQCIntro HTML
Reference Manual PDF
NEWS Text

Details

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 (http://pandoc.org/installing.html) for generating reports from markdown files.
URL https://github.com/mani2012/BatchQC
Bug Reports https://github.com/mani2012/BatchQC/issues
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BatchQC_1.30.0.tar.gz
Windows Binary BatchQC_1.30.0.zip
macOS Binary (x86_64) BatchQC_1.30.0.tgz
macOS Binary (arm64) BatchQC_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BatchQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BatchQC
Bioc Package Browser https://code.bioconductor.org/browse/BatchQC/
Package Short Url https://bioconductor.org/packages/BatchQC/
Package Downloads Report Download Stats