GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

• Jason S. Cumbie ,

  Contributed equally to this work with: Jason S. Cumbie, Jeffrey A. Kimbrel

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America

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• Jeffrey A. Kimbrel ,

  Contributed equally to this work with: Jason S. Cumbie, Jeffrey A. Kimbrel

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America

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• Yanming Di,

  Affiliation Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America

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• Daniel W. Schafer,

  Affiliation Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America

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• Larry J. Wilhelm,

  Current address: Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon, United States of America

  Affiliation Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

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• Samuel E. Fox,

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America

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• Christopher M. Sullivan,

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America

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• Aron D. Curzon,

  Affiliation Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

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• James C. Carrington,

  Current address: Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America

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• Todd C. Mockler,

  Current address: Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America

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• Jeff H. Chang

  * E-mail: changj@cgrb.oregonstate.edu

  Affiliations Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America, Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America

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