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My (mostly) java sources at the Center for studies of the Human Polymorphism (CEPH). Fondation. Jean Dausset
Statistical tools developed for the the encode consortium. Currently, there are two tools. Overlap Statistics - Calculate the statistical significance of two genomic regions. Segmentation - Segment genomic regions into homogenous subregions. The code and docs can be downloaded at http://encode.dyndns.org/