{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T05:13:45Z","timestamp":1778822025690,"version":"3.51.4"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":90,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01 HG005692, R01 ES025002"],"award-info":[{"award-number":["R01 HG005692, R01 ES025002"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["DGE 0654108"],"award-info":[{"award-number":["DGE 0654108"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>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 \u2018-omics\u2019 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.<\/jats:p>\n                  <jats:p>Availability and Implementation: BatchQC is available through Bioconductor: http:\/\/bioconductor.org\/packages\/BatchQC and GitHub: https:\/\/github.com\/mani2012\/BatchQC.<\/jats:p>\n                  <jats:p>Contact: \u00a0wej@bu.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw538","type":"journal-article","created":{"date-parts":[[2016,8,18]],"date-time":"2016-08-18T21:19:13Z","timestamp":1471555153000},"page":"3836-3838","source":"Crossref","is-referenced-by-count":62,"title":["BatchQC: interactive software for evaluating sample and batch effects in genomic data"],"prefix":"10.1093","volume":"32","author":[{"given":"Solaiappan","family":"Manimaran","sequence":"first","affiliation":[{"name":"1Department of Biostatistics, Boston University, Boston, MA"},{"name":"2Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heather Marie","family":"Selby","sequence":"additional","affiliation":[{"name":"3Bioinformatics Program, Boston University, Boston, MA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwame","family":"Okrah","sequence":"additional","affiliation":[{"name":"4gRED Oncology Biostatistics, Genentech, South San Francisco, CA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claire","family":"Ruberman","sequence":"additional","affiliation":[{"name":"5Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey T.","family":"Leek","sequence":"additional","affiliation":[{"name":"5Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Quackenbush","sequence":"additional","affiliation":[{"name":"6Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA"},{"name":"7Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin","family":"Haibe-Kains","sequence":"additional","affiliation":[{"name":"8Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada"},{"name":"9Princess Margaret Cancer Centre, University Health NetworkToronto, Ontario, Canada"},{"name":"10Ontario Institute of Cancer Research, Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hector Corrada","family":"Bravo","sequence":"additional","affiliation":[{"name":"11Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W. 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