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Yet, current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false-positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here, we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false-positive findings.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Dream is available within the variancePartition Bioconductor package at http:\/\/bioconductor.org\/packages\/variancePartition.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>gabriel.hoffman@mssm.edu<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa687","type":"journal-article","created":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T15:15:12Z","timestamp":1595517312000},"page":"192-201","source":"Crossref","is-referenced-by-count":279,"title":["Dream: powerful differential expression analysis for repeated measures designs"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0957-0224","authenticated-orcid":false,"given":"Gabriel E","family":"Hoffman","sequence":"first","affiliation":[{"name":"Icahn School of Medicine at Mount Sinai Pamela Sklar Division of Psychiatric Genomics, , New York, NY 10029, USA"},{"name":"Icahn School of Medicine at Mount Sinai Icahn Institute for Data Science and Genomic Technology, , New York, NY 10029, USA"},{"name":"Icahn School of Medicine at Mount Sinai Department of Genetics and Genomic Sciences, , New York, NY 10029, USA"}]},{"given":"Panos","family":"Roussos","sequence":"additional","affiliation":[{"name":"Icahn School of Medicine at Mount Sinai Pamela Sklar Division of Psychiatric Genomics, , New York, NY 10029, USA"},{"name":"Icahn School of Medicine at Mount Sinai Icahn Institute for Data Science and Genomic Technology, , New York, NY 10029, USA"},{"name":"Icahn School of Medicine at Mount Sinai Department of Genetics and Genomic Sciences, , New York, NY 10029, USA"},{"name":"Icahn School of Medicine at Mount Sinai Department of Psychiatry, , New York, NY 10029, USA"},{"name":"Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. 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