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BatchQC

This is the development version of BatchQC; for the stable release version, see BatchQC.

Batch Effects Quality Control Software


Bioconductor version: Development (3.19)

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: Jessica McClintock [aut, cre] , W. Evan Johnson [aut] , 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 [aut]

Maintainer: Jessica McClintock <jessica.mcclintock at rutgers.edu>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 R Script
Introdution to BatchQC HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BatchEffect, DifferentialExpression, GraphAndNetwork, ImmunoOncology, Microarray, Normalization, Preprocessing, PrincipalComponent, QualityControl, RNASeq, Sequencing, Software, Visualization
Version 1.99.00
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale, ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, stats, SummarizedExperiment, sva, tibble, tidyr, tidyverse, utils
System Requirements
URL https://github.com/wejlab/BatchQC
Bug Reports https://github.com/wejlab/BatchQC/issues
See More
Suggests BiocManager, BiocStyle, bladderbatch, dendextend, devtools, knitr, lintr, plotly, rmarkdown, shinythemes, spelling, testthat (>= 3.0.0)
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package BatchQC_1.99.00.tar.gz
Windows Binary BatchQC_1.99.00.zip (64-bit only)
macOS Binary (x86_64) BatchQC_1.99.00.tgz
macOS Binary (arm64) BatchQC_1.99.00.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