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This app is a wrapper of the exploBATCH, an R package for evaluating and correcting for batch effect in genomic studies.
Please read the following refererence for more details on exploBATCH
Sci Rep. 2017 Sep 7;7(1):10849. doi: 10.1038/s41598-017-11110-6. A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies.
The comBat method is decribed in SVA package. Here we used the parameter option
Please read the following refererence for more details on exploBATCH
Sci Rep. 2017 Sep 7;7(1):10849. doi: 10.1038/s41598-017-11110-6. A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies.
The comBat method is decribed in SVA package. Here we used the parameter option
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Data table pre-process
Original Data
Processed Data
Expression matrix
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Meta data
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About
This app is a simple wrapper for the exploBATCH
refer to https://github.com/syspremed/exploBATCH for more details
Contact
Acknowledgement
This shiny apps uses:
DT, data.table: to table manipulation and display
shinyBS: for progressing status.
plotly: to make ggplot2 plot more interactive
ggplot2: for a lot of plotting
Of course, shiny, rstudio, htmlwidgets, and many more
ChangeLog
V0.2: 20180214, add comBat only mode with parameter correction, and UI adjust and a bug fix to increase the speed
V0.11: 20180207, a few bug fix and more preprocess options added
V0.1: 20180206, app online
V0.11: 20180207, a few bug fix and more preprocess options added
V0.1: 20180206, app online