TY - JOUR T1 - Differential abundance analysis for microbial marker-gene surveys JF - Nature methods Y1 - 2013 A1 - Joseph N. Paulson A1 - Stine, O. Colin A1 - Héctor Corrada Bravo A1 - M. Pop AB - We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling—a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field. PB - Nature Publishing Group VL - 10 SN - 1548-7091 UR - http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html M3 - 10.1038/nmeth.2658 ER -