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Flexible isoform-level differential expression analysis with Ballgown

Alyssa C. Frazee, Geo Pertea, Andrew E. Jaffe, Ben Langmead, Steven L. Salzberg, Jeffrey T. Leek
doi: https://doi.org/10.1101/003665
Alyssa C. Frazee
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
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Geo Pertea
2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine
3Center for Computational Biology, Johns Hopkins University
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Andrew E. Jaffe
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
3Center for Computational Biology, Johns Hopkins University
4Lieber Institute for Brain Development, Johns Hopkins Medical Campus
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Ben Langmead
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine
3Center for Computational Biology, Johns Hopkins University
5Department of Computer Science, Johns Hopkins University
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Steven L. Salzberg
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine
3Center for Computational Biology, Johns Hopkins University
5Department of Computer Science, Johns Hopkins University
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Jeffrey T. Leek
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
3Center for Computational Biology, Johns Hopkins University
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  • For correspondence: jtleek@gmail.com
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Abstract

We have built a statistical package called Ballgown for estimating differential expression of genes, transcripts, or exons from RNA sequencing experiments. Ballgown is designed to work with the popular Cufflinks transcript assembly software and uses well-motivated statistical methods to provide estimates of changes in expression. It permits statistical analysis at the transcript level for a wide variety of experimental designs, allows adjustment for confounders, and handles studies with continuous covariates. Ballgown provides improved statistical significance estimates as compared to the Cuffdiff2 differential expression tool included with Cufflinks. We demonstrate the flexibility of the Ballgown package by re-analyzing 667 samples from the GEUVADIS study to identify transcript-level eQTLs and identify non-linear artifacts in transcript data. Our package is freely available from: https://github.com/alyssafrazee/ballgown

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 30, 2014.
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Flexible isoform-level differential expression analysis with Ballgown
Alyssa C. Frazee, Geo Pertea, Andrew E. Jaffe, Ben Langmead, Steven L. Salzberg, Jeffrey T. Leek
bioRxiv 003665; doi: https://doi.org/10.1101/003665
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Flexible isoform-level differential expression analysis with Ballgown
Alyssa C. Frazee, Geo Pertea, Andrew E. Jaffe, Ben Langmead, Steven L. Salzberg, Jeffrey T. Leek
bioRxiv 003665; doi: https://doi.org/10.1101/003665

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