There is a large array of different genome browsers, each with its own characteristics. Obviously a lot of work has been put into developing these. However, I was surprised that I could not find any genome browser that supports visualization of 2d genomic data as well as 1d genomic data (genomic tracks). Does anyone know of such genome browsers?
By 2d genomic data I mean any quantitative data which is assigned to pairs of genomic locations, and would often be visualized as a heatmap (as Istvan suggested, this can be also interpreted as 3d data). An example of 2d genomic data would be calculation of linkage disequilbrium between pairs of loci. This is just one example of 2d data, I want to be able to visualize my own 2d datasets (not LD) in parallel.
I would prefer a fast offline genome browser (not web-based) with extensive customization options, if such a browser exists.