To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("BatchQC")

In most cases, you don't need to download the package archive at all.

BatchQC

 

   

Batch Effects Quality Control Software

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("BatchQC")

Documentation

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

browseVignettes("BatchQC")

 

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

Details

biocViews BatchEffect, DifferentialExpression, GraphAndNetwork, Microarray, Preprocessing, PrincipalComponent, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License GPL (>= 2)
Depends R (>= 3.3.0)
Imports utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva, corpcor, moments, matrixStats, ggvis, d3heatmap, 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 PathoStat
Suggests Me
Build Report  

Package Archives

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

Package Source BatchQC_1.4.0.tar.gz
Windows Binary BatchQC_1.4.0.zip
Mac OS X 10.11 (El Capitan) BatchQC_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BatchQC/tree/release-3.5
Package Short Url http://bioconductor.org/packages/BatchQC/
Package Downloads Report Download Stats

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