Differential analysis of RNA-seq incorporating quantification uncertainty

@article{Pimentel2017DifferentialAO,
  title={Differential analysis of RNA-seq incorporating quantification uncertainty},
  author={Harold Pimentel and Nicolas L. Bray and Suzette Puente and P{\'a}ll Melsted and Lior Pachter},
  journal={Nature Methods},
  year={2017},
  volume={14},
  pages={687-690}
}
We describe sleuth (http://pachterlab.github.io/sleuth), a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. sleuth is implemented in an interactive shiny app that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of data from RNA-seq experiments. 

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