QC module

This release adds a quality control module to check the results from hicBuildMatrix. By default, now hicBuildMatrix generates a HTML page containing the plots from the QC measures. The results from several runs of hicBuildMatrix can be combined in one page using the new tool hicQC.

Also, this release added a module called hicCompareMatrices that takes two Hi-C matrices and computes the difference, the ratio or the log2 ratio. The resulting matrix can be plotted with hicPlotMatrix to visualize the changes.

Small bugfix release

Merge pull request #68 from maxplanck-ie/docs

Docs

release 1.6

This release introduces an updated method to call TADs that requires less parameters.

1.5

removed unnecesary parameter `fragmentLength` from hicBuildMatrix

X-mas madness release

• plotting improvements all over
• new HiCInfo tool

The Sunday release

Merge pull request #38 from maxplanck-ie/plotting_fixes

Fix plotting on HPC

Added support for long reads

Mostly, this release addresses issues with long reads (over 75 bp long) that often contain a restriction site within.

This new release, handles those chimeric reads. Furthermore, the hic-matrix creation output is now more informative.