This release fixes a problem related to python3 in which chromosome names were of bytes type.

The 2.1 version of HiCExplorer comes with new features and bugfixes.

• Adding the new feature hicAggregateContacts: A tool that allows plotting of aggregated Hi-C sub-matrices of a specified list of positions.
• Many improvements to the documentation and the help text. Thanks to @GinaRe and @gtrichard.
• hicPlotMatrix:
  • supports only bigwig files for an additional data track.
  • the argument --pca was renamed to --bigwig
  • Smoothing the bigwig values to neighboring bins if no data is present there
  • Fixes to a bug concerning a crash of tight_layout
  • Adding the possibility to flip the sign of the values of the bigwig track
  • Adding the possibility to scale the values of the bigwig track
• hicPlotViewpoint: Adds a feature to plot multiple matrices in one image
• cooler file format:
  • supports mcool files
  • applies correction factors if present
  • optionally reads bin['weight']
• fixes:
  • a crash in hicPlotTads if horizontal lines were used
  • checks if all characters of a title are ASCII. If not they are converted to the closest looking one.
• Updated and fixate version number of the dependencies

This pre-release contains:

• many bugfixes
• an improved documentation
• the new feature hicAggregateContacts
• support for mcool files

This release brings the following new features:

• Python 3.6 support
• cooler file format support
• PCA computation for A / B compartment
• visualizations of viewpoints
• many bug fixes
• change license to GPLv3

Small improvements concerning matrix file format detection which makes it easier with Galaxy wrapper.

Release 2.0 will bring new features:

• Python 3.6 support
• cooler file format support
• PCA computation for A / B compartment
• visualizations of viewpoints
• many bug fixes

• Thanks to Aleksander Jankowski for fixing the handling of chimeric alignments in hicBuildMatrix (PR #151). Now, for reads with supplementary alignments, only the alignment closer to the 5' end
  of the read is used.

• We discovered that the handling of dangling ends was too strict as all reads starting with the dangling sequence were considered dangling ends (#152). However, a read frequently could start with the dangling sequence but otherwise have a mate from a proper Hi-C re-ligation. Thus, we now only count reads as 'dangling ends' if the mates are within the maximum library insert size distance, face inwards and one of them starts with the dangling sequence.

• As part of this release we also improved the help message of hicBuildMatrix. For this, we replaced the --maxDistance parameter by --maxLibraryInsertSize, which should be based on the measured insert size of the Hi-C library.

This release is adding new features and fixes many bugs:

• hicBuildMatrix: Added multicore support, new parameters --threads and --inputBufferSize
• hicFindTADs:
  • One call instead of two: hicFindTADs TAD_score and hicFindTADs find_TADs merged to hicFindTADs.
  • New multiple correction method supported: False discovery rate. Call it with --correctForMultipleTesting fdr and --threshold 0.05.
• Update of the tutorial: mES-HiC analysis.
• Additional test cases and docstrings to improve the software quality
• Fixed a bug occurring with bigwig files with frequent NaN values which resulted in only NaN averages
• hicPlotTADs: Support for plotting points
• Moved galaxy wrappers to https://github.com/galaxyproject/tools-iuc
• Fixed multiple bugs with saving matrices
• hicCorrelate: Changes direction of dendograms to left

• Various cleanups
• Added option to plot bigwig files as a line in hicPlotTADs
• Updated documentation
• Improved hicPlotMatrix --region output
• Added compressed matrices. In our tests the compressed matrices are significantly smaller.
• hicPlotDistVsCount can now use multiple matrices
• Galaxy wrapper enhancements

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.