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BEclear-CL

Description

Correction of batch effects with BEclear as a command line tool. If you have any issues regarding the core program, please visit the originial BEclear repository.

Installation

git clone git@github.com:uds-helms/BEclear-CL.git
cd BEclear-CL
## check and install required packages
Rscript install_requirements.R
chmod +x BEclearCL.R

Usage example

Accessing the help pages:

./BEclearCL.R -h

Simple usage example:

./BEclearCL.R -f testDataSet.txt -o testImputed.txt -s testSamples.txt

Using BEclearCL in a pipeline:

cat test.txt | ./BEclearCL.R -w

Additional Help

A more detailed description of the tool can be found in the Documentation.pdf.

Citation

Akulenko, R., Merl, M., & Helms, V. (2016). BEclear: Batch effect detection and adjustment in DNA methylation data. PLoS ONE, 11(8), 1–17. https://doi.org/10.1371/journal.pone.0159921