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BatchServer: a web server for batch effect evaluation, visualization and correction

By Tiansheng Zhu, Guo-Bo Chen, Chunhui Yuan, Rui Sun, Fangfei Zhang, Xiao Yi, Shuigen Zhou, Tiannan Guo

Posted 25 Mar 2020
bioRxiv DOI: 10.1101/2020.03.23.996264

Batch effects are unwanted data variations that may obscure biological signals, leading to bias or errors in subsequent data analyses. Effective evaluation and elimination of batch effects are necessary for omics data analysis. In order to facilitate the evaluation and correction of batch effects, here we present BatchSever, an open-source R/Shiny based user-friendly interactive graphical web platform for batch effects analysis. In BatchServer we introduced autoComBat, a modified version of ComBat, which is the most widely adopted tool for batch effect correction. BatchServer uses PVCA (Principal Variance Component Analysis) and UMAP (Manifold Approximation and Projection) for evaluation and visualizion of batch effects. We demonstate its application in multiple proteomics and transcriptomic data sets. BatchServer is provided at <https://lifeinfo.shinyapps.io/batchserver/> as a web server. The source codes are freely available at <https://github.com/guomics-lab/batch_server>. ### Competing Interest Statement The authors have declared no competing interest. * MS : mass spectrometry NGS : next generation sequencing PCA : principal components analysis PVCA : Principal Variance Component Analysis UMAP : Manifold Approximation and Projection SVD : Singular Value Decomposition t-SNE : t-distributed stochastic neighbor embedding K-S test : Kolmogorov–Smirnov test DIA : data independent acquisition.

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