BatchQC

DOI: 10.18129/B9.bioc.BatchQC    

Batch Effects Quality Control Software

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML		BatchQC_examples
PDF	R Script	BatchQC_usage_advanced
HTML		BatchQCIntro
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, DifferentialExpression, GraphAndNetwork, ImmunoOncology, Microarray, Preprocessing, PrincipalComponent, QualityControl, RNASeq, Sequencing, Software, Visualization
Version	1.20.0
In Bioconductor since	BioC 3.3 (R-3.3) (5.5 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
LinkingTo
Suggests	testthat
SystemRequirements	pandoc (http://pandoc.org/installing.html) for generating reports from markdown files.
Enhances
URL	https://github.com/mani2012/BatchQC
BugReports	https://github.com/mani2012/BatchQC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BatchQC_1.20.0.tar.gz
Windows Binary	BatchQC_1.20.0.zip
macOS 10.13 (High Sierra)	BatchQC_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BatchQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BatchQC
Package Short Url	https://bioconductor.org/packages/BatchQC/
Package Downloads Report	Download Stats