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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BatchQC")
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>
Bioconductor views BatchEffect DifferentialExpression GraphAndNetwork Microarray Preprocessing PrincipalComponent QualityControl RNASeq Sequencing Software Visualization
Date of publicationNone
MaintainerSolaiappan Manimaran <manimaran_1975@hotmail.com>
LicenseGPL (>= 2)
Version1.4.0
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

Functions

batch_indicator Man page
batchQC Man page
batchQC_analyze Man page
batchqc_circosplot Man page
batchQC_condition_adjusted Man page
batchqc_correlation Man page
batchqc_corscatter Man page
batchqc_explained_variation Man page
batchQC_filter_genes Man page
batchQC_fsva_adjusted Man page
batchqc_heatmap Man page
batchQC_num.sv Man page
BatchQCout-class Man page
batchqc_pca Man page
batchqc_pca_svd Man page
batchqc_pc_explained_variation Man page
batchQC_shapeVariation Man page
batchQC_sva Man page
batchQC_svregress_adjusted Man page
batchtest Man page
combatPlot Man page
example_batchqc_data Man page
getShinyInput Man page
getShinyInputCombat Man page
getShinyInputOrig Man page
getShinyInputSVA Man page
getShinyInputSVAf Man page
getShinyInputSVAr Man page
gnormalize Man page
log2CPM Man page
makeSVD Man page
pcRes Man page
plotPC Man page
protein_data Man page
protein_example_data Man page
protein_sample_info Man page
rnaseq_sim Man page
setShinyInput Man page
setShinyInputCombat Man page
setShinyInputOrig Man page
setShinyInputSVA Man page
setShinyInputSVAf Man page
setShinyInputSVAr Man page
signature_data Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.