BatchQC: interactive software for evaluating sample and batch effects in genomic data

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BatchQC: interactive software for evaluating sample and batch effects in genomic data

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Title: BatchQC: interactive software for evaluating sample and batch effects in genomic data
Author: Manimaran, Solaiappan; Selby, Heather Marie; Okrah, Kwame; Ruberman, Claire; Leek, Jeffrey T.; Quackenbush, John; Haibe-Kains, Benjamin; Bravo, Hector Corrada; Johnson, W. Evan

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Citation: 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.
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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.
Published Version: doi:10.1093/bioinformatics/btw538
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167063/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:29739133
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