BatchQC: interactive software for evaluating sample and batch effects in genomic data.
BatchQC: interactive software for evaluating sample and batch effects in genomic data.
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DOI：
10.1093/bioinformatics/btw538
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发表时间：
2016-12-15
期刊：
影响因子：
--
通讯作者：
Johnson WE
中科院分区：
文献类型：
--
作者：
Manimaran S;Selby HM;Okrah K;Ruberman C;Leek JT;Quackenbush J;Haibe-Kains B;Bravo HC;Johnson WE
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.
影响因子：
2.1
作者：
Johnson, W. Evan;Li, Cheng;Rabinovic, Ariel
通讯作者：
Rabinovic, Ariel
影响因子：
5.8
作者：
Leek, Jeffrey T.;Johnson, W. Evan;Storey, John D.
通讯作者：
Storey, John D.
影响因子：
2.1
作者：
Okrah, Kwame;Bravo, Hector Corrada
通讯作者：
Bravo, Hector Corrada