PASS (Poisson Approximation for Statistical Significance) is a software that can accurately control the FDR level in ChIP data analysis. The method is designed for detecting transcription factor binding, and may not work well for wide spread signals such as nucleopositioning data. If the data is from ChIP-seq, you need to convert each ChIP-seq value into z-scores before using this program.
CoCAS is a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application. It has been designed to be used primarily on Agilent microarrays scanned with an Agilent scanner.
CoCAS can readily be used on the latest generation of Agilent high-density arrays. Unlike other tools available, Cocas allows dye-swap, replicate correlation and connects easily with other software (genome browsers and peak detection). The peak detection methods implemented in CoCAS can be used for any set of data including ChIP-Seq data.