BatchQC: interactive software for evaluating sample and batch effects in genomic data
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Author
Manimaran, Solaiappan
Selby, Heather Marie
Okrah, Kwame
Ruberman, Claire
Leek, Jeffrey T.
Haibe-Kains, Benjamin
Bravo, Hector Corrada
Johnson, W. Evan
Published Version
https://doi.org/10.1093/bioinformatics/btw538Metadata
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Manimaran, Solaiappan, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Hector Corrada Bravo, and W. Evan Johnson. 2016. “BatchQC: interactive software for evaluating sample and batch effects in genomic data.” Bioinformatics 32 (24): 3836-3838. doi:10.1093/bioinformatics/btw538. http://dx.doi.org/10.1093/bioinformatics/btw538.Abstract
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. There are several existing batch adjustment tools for ‘-omics’ data, but they do not indicate a priori whether adjustment needs to be conducted or how correction should be applied. We present a software pipeline, BatchQC, which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset. BatchQC can also apply existing adjustment tools and allow users to evaluate their benefits interactively. We used the BatchQC pipeline on both simulated and real data to demonstrate the effectiveness of this software toolkit. Availability and Implementation: BatchQC is available through Bioconductor: http://bioconductor.org/packages/BatchQC and GitHub: https://github.com/mani2012/BatchQC. Contact: wej@bu.edu Supplementary information: Supplementary data are available at Bioinformatics online.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167063/pdf/Terms of Use
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