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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

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Data table pre-process

Q vaule is the presence percentage threshold. For example, 0,75 means 75% of presence across all samples
This function centers and scales numeric matrix. Center means the data(row or column)'s mean is going to be 0. Scale is done after centering. Scale is done by divding each value by their standard deviation. This function is called z-score some elsewhere.

Original Data

Processed Data

Expression matrix

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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

Author: Zhibin Ning
Email: ningzhibin@gmail.com
Suggestions and bug report

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