Abstract Automated Genomics Analysis (AGA) is a program to analyze high-throughput genomic data sets, such as Affymetrix gene expression arrays. The software implements an easy to use, point and click, guided pipeline to combine, define and compare datasets, and customize their outputs. Batch correction techniques are implemented to combine data sets. Options to save plots, tables and data are available throughout the analysis, and log files containing the R script run are also generated to facilitate reproducible analyses. The software has been applied to gene expression measurements from head and neck squamous cell carcinoma (HNSCC). It has batch corrected several public domain microarray HNSCC datasets, facilitating accurate comparison of subtypes such as HPV status. Moreover, current extensions enable users to interactively perform reproducible genomics analysis using clinical covariates in RNA sequencing data from TCGA. Citation Format: Michael Considine, Hilary S. Parker, Yingying Wei, Xiao X. Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig. Interactive pipeline for reproducible genomics analyses. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-317. doi:10.1158/1538-7445.AM2014-LB-317