BatchQC: Batch Effects Quality Control Software

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.

AuthorSolaiappan 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 publicationNone
MaintainerSolaiappan Manimaran <manimaran_1975@hotmail.com>
LicenseGPL (>= 2)
Version1.2.1
https://github.com/mani2012/BatchQC

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

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