BatchQC: Batch Effects Quality Control Software

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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@hotmail.com>, W. Evan Johnson <wej@bu.edu>, Heather Selby <selbyh@bu.edu>, Claire Ruberman <claireruberman@gmail.com>, Kwame Okrah <kwame.okrah@gmail.com>, Hector Corrada Bravo <hcorrada@gmail.com>
Date of publication
None
Maintainer
Solaiappan Manimaran <manimaran_1975@hotmail.com>
License
GPL (>= 2)
Version
1.2.1
URLs

View on Bioconductor

Man pages

batchQC
Checks for presence of batch effect and creates a html report...
batchQC_analyze
Checks for presence of batch effect and reports whether the...
batchqc_circosplot
Produce Circos plot
batchQC_condition_adjusted
Returns adjusted data after remove the variation across...
batchqc_correlation
Produce correlation heatmap plot
batchqc_corscatter
Produce Median Correlation plot
batchqc_explained_variation
Returns a list of explained variation by batch and condition...
batchQC_filter_genes
Returns a datset after filtering genes of zero variance...
batchQC_fsva_adjusted
Use frozen surrogate variable analysis to remove the...
batchqc_heatmap
Produce heatmap plots for the given data
batchQC_num.sv
Returns the number of surrogate variables to estimate in the...
BatchQCout-class
The BatchQC output class to output BatchQC results
batchqc_pca
Performs principal component analysis and produces plot of...
batchqc_pca_svd
Performs PCA svd variance decomposition and produces plot of...
batchqc_pc_explained_variation
Returns explained variation for each principal components
batchQC_shapeVariation
Perform Mean and Variance batch variation analysis
batchQC_sva
Estimate the surrogate variables using the 2 step approach...
batchQC_svregress_adjusted
Regress the surrogate variables out of the expression data
batchtest
Performs test to check whether batch needs to be adjusted
combatPlot
Adjust for batch effects using an empirical Bayes framework...
example_batchqc_data
Batch and Condition indicator for signature data captured...
getShinyInput
Getter function to get the shinyInput option
getShinyInputCombat
Getter function to get the shinyInputCombat option
getShinyInputOrig
Getter function to get the shinyInputOrig option
getShinyInputSVA
Getter function to get the shinyInputSVA option
getShinyInputSVAf
Getter function to get the shinyInputSVAf option
getShinyInputSVAr
Getter function to get the shinyInputSVAr option
gnormalize
Perform Genewise Normalization of the given data matrix
log2CPM
Compute log2(counts per mil reads) and library size for each...
makeSVD
Compute singular value decomposition
pcRes
Compute variance of each principal component and how they...
plotPC
Plot first 2 principal components
protein_example_data
Batch and Condition indicator for protein expression data
rnaseq_sim
Generate simulated count data with batch effects for ngenes
setShinyInput
Setter function to set the shinyInput option
setShinyInputCombat
Setter function to set the shinyInputCombat option
setShinyInputOrig
Setter function to set the shinyInputOrig option
setShinyInputSVA
Setter function to set the shinyInputSVA option
setShinyInputSVAf
Setter function to set the shinyInputSVAf option
setShinyInputSVAr
Setter function to set the shinyInputSVAr option

Files in this package

BatchQC/DESCRIPTION
BatchQC/NAMESPACE
BatchQC/R
BatchQC/R/Circos.R
BatchQC/R/batchQC.R
BatchQC/R/batchtest.R
BatchQC/R/correlation.R
BatchQC/R/heatmap.R
BatchQC/R/pca.R
BatchQC/R/shapeAnalysis.R
BatchQC/R/simulate_data.R
BatchQC/R/sva.R
BatchQC/R/utils.R
BatchQC/README.md
BatchQC/build
BatchQC/build/vignette.rds
BatchQC/data
BatchQC/data/example_batchqc_data.rda
BatchQC/data/protein_example_data.rda
BatchQC/inst
BatchQC/inst/CITATION
BatchQC/inst/NEWS.Rd
BatchQC/inst/doc
BatchQC/inst/doc/BatchQCIntro.Rmd
BatchQC/inst/doc/BatchQCIntro.html
BatchQC/inst/doc/BatchQC_examples.Rmd
BatchQC/inst/doc/BatchQC_examples.html
BatchQC/inst/doc/BatchQC_usage_advanced.R
BatchQC/inst/doc/BatchQC_usage_advanced.Rmd
BatchQC/inst/doc/BatchQC_usage_advanced.pdf
BatchQC/inst/example
BatchQC/inst/example/batchqc_combat_adj_report.html
BatchQC/inst/example/batchqc_pipeline.R
BatchQC/inst/example/batchqc_report.html
BatchQC/inst/reports
BatchQC/inst/reports/batchQC.html
BatchQC/inst/reports/batchqc_report.Rmd
BatchQC/inst/reports/libs
BatchQC/inst/reports/libs/bootstrap
BatchQC/inst/reports/libs/bootstrap/css
BatchQC/inst/reports/libs/bootstrap/css/bootstrap-responsive.min.css
BatchQC/inst/reports/libs/bootstrap/css/bootstrap.min.css
BatchQC/inst/reports/libs/bootstrap/css/user.css
BatchQC/inst/reports/libs/bootstrap/javascript
BatchQC/inst/reports/libs/bootstrap/javascript/bootstrap.min.js
BatchQC/inst/reports/libs/bootstrap/javascript/jquery-1.10.1.min.js
BatchQC/inst/reports/libs/bootstrap/javascript/user.js
BatchQC/inst/rmarkdown
BatchQC/inst/rmarkdown/templates
BatchQC/inst/rmarkdown/templates/batchqc
BatchQC/inst/rmarkdown/templates/batchqc/skeleton
BatchQC/inst/rmarkdown/templates/batchqc/skeleton/skeleton.Rmd
BatchQC/inst/rmarkdown/templates/batchqc/template.yaml
BatchQC/inst/shiny
BatchQC/inst/shiny/BatchQC
BatchQC/inst/shiny/BatchQC/server.R
BatchQC/inst/shiny/BatchQC/ui.R
BatchQC/man
BatchQC/man/BatchQCout-class.Rd
BatchQC/man/batchQC.Rd
BatchQC/man/batchQC_analyze.Rd
BatchQC/man/batchQC_condition_adjusted.Rd
BatchQC/man/batchQC_filter_genes.Rd
BatchQC/man/batchQC_fsva_adjusted.Rd
BatchQC/man/batchQC_num.sv.Rd
BatchQC/man/batchQC_shapeVariation.Rd
BatchQC/man/batchQC_sva.Rd
BatchQC/man/batchQC_svregress_adjusted.Rd
BatchQC/man/batchqc_circosplot.Rd
BatchQC/man/batchqc_correlation.Rd
BatchQC/man/batchqc_corscatter.Rd
BatchQC/man/batchqc_explained_variation.Rd
BatchQC/man/batchqc_heatmap.Rd
BatchQC/man/batchqc_pc_explained_variation.Rd
BatchQC/man/batchqc_pca.Rd
BatchQC/man/batchqc_pca_svd.Rd
BatchQC/man/batchtest.Rd
BatchQC/man/combatPlot.Rd
BatchQC/man/example_batchqc_data.Rd
BatchQC/man/getShinyInput.Rd
BatchQC/man/getShinyInputCombat.Rd
BatchQC/man/getShinyInputOrig.Rd
BatchQC/man/getShinyInputSVA.Rd
BatchQC/man/getShinyInputSVAf.Rd
BatchQC/man/getShinyInputSVAr.Rd
BatchQC/man/gnormalize.Rd
BatchQC/man/log2CPM.Rd
BatchQC/man/makeSVD.Rd
BatchQC/man/pcRes.Rd
BatchQC/man/plotPC.Rd
BatchQC/man/protein_example_data.Rd
BatchQC/man/rnaseq_sim.Rd
BatchQC/man/setShinyInput.Rd
BatchQC/man/setShinyInputCombat.Rd
BatchQC/man/setShinyInputOrig.Rd
BatchQC/man/setShinyInputSVA.Rd
BatchQC/man/setShinyInputSVAf.Rd
BatchQC/man/setShinyInputSVAr.Rd
BatchQC/tests
BatchQC/tests/testthat
BatchQC/tests/testthat.R
BatchQC/tests/testthat/test_batchQC.R
BatchQC/vignettes
BatchQC/vignettes/BatchQCIntro.Rmd
BatchQC/vignettes/BatchQC_examples.Rmd
BatchQC/vignettes/BatchQC_usage_advanced.Rmd