Differential abundance analysis for microbial marker-gene surveys

TitleDifferential abundance analysis for microbial marker-gene surveys
Publication TypeJournal Articles
Year of Publication2013
AuthorsPaulson JN, O. Stine C, Bravo HCorrada, Pop M.
JournalNature methods
Start Page1200
ISBN Number1548-7091

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.