PT - JOURNAL ARTICLE AU - Harold Pimentel AU - Bray Nicolas L. AU - Suzette Puente AU - Páll Melsted AU - Lior Pachter TI - Differential analysis of RNA-Seq incorporating quantification uncertainty AID - 10.1101/058164 DP - 2016 Jan 01 TA - bioRxiv PG - 058164 4099 - http://biorxiv.org/content/early/2016/06/10/058164.short 4100 - http://biorxiv.org/content/early/2016/06/10/058164.full AB - We describe a novel method for the differential analysis of RNA-Seq data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. The method is implemented in an interactive shiny app called sleuth that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of RNA-Seq experiments.