The documentation release

The second bug fix release of 2.1 includes:

• documentation improvements
• fixing broken Readthedocs documentation
• Small bug fix concerning hicPlotMatrix and cooler: --chromosomeOrder is now possible with more than one chromosome
• Small fixes concerning updated dependencies: Fixing version number a bit more specific and not that strict in test cases delta values.

fix chromosome names in python3

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

March release

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

HiCExplorer 2.1 alpha

This pre-release contains:

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

Winter release

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

HiCExplorer 2. 0 release candidate 2

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

HiCExplorer 2.0 release candidate

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

dangling ends and supplementary alignments

• 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.

Autumn release

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

Compressed matrices

• 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