{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T18:05:28Z","timestamp":1776276328095,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data\/models accommodated by the software and (iii) low power of common multiple testing approaches.<\/jats:p>\n               <jats:p>Results: The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation.<\/jats:p>\n               <jats:p>Conclusion: Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies.<\/jats:p>\n               <jats:p>Availability and implementation: The cit open-source R package is freely available from the CRAN website (https:\/\/cran.r-project.org\/web\/packages\/cit\/index.html) with embedded C\u2009++\u2009code that utilizes the GNU Scientific Library, also freely available (http:\/\/www.gnu.org\/software\/gsl\/).<\/jats:p>\n               <jats:p>Contact: \u00a0joshua.millstein@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw135","type":"journal-article","created":{"date-parts":[[2016,3,11]],"date-time":"2016-03-11T01:49:10Z","timestamp":1457660950000},"page":"2364-2365","source":"Crossref","is-referenced-by-count":56,"title":["cit: hypothesis testing software for mediation analysis in genomic applications"],"prefix":"10.1093","volume":"32","author":[{"given":"Joshua","family":"Millstein","sequence":"first","affiliation":[{"name":"Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary K.","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carrie V.","family":"Breton","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,3,9]]},"reference":[{"key":"2023020112480011300_btw135-B1","doi-asserted-by":"crossref","first-page":"6304","DOI":"10.1038\/ncomms7304","article-title":"Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children","volume":"6","author":"Hong","year":"2015","journal-title":"Nat. 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