Flexible analysis of transcriptome assemblies with Ballgown

We have built a statistical package called Ballgown for estimating dierential expression of genes, transcripts, or exons from RNA sequencing experiments. Ballgown is designed to work with the popular Cuinks 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 signicance estimates as compared to the

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