ANAIS is a user-friendly web-based tool for the processing of NimbleGen expression data. The interface reads single-channel microarray files generated by NimbleGen platforms and produces easily interpretable graphical and numerical results. It provides biologists six turnkey analysis modules-normalization, probe to gene, quality controls, differential expression, detection, queries and clustering-to explore quickly, freely and without the need for computer programming, NimbleGen transcriptome data.