April bug fix release 2

• Pinning dependencies to:

  • hicmatrix version 9: API changes in version 10
  • krbalancing version 0.0.4: API changes in version 0.0.5
  • matplotlib version 3.0: Version 3.1 raises 'Not implemented error' for unknown reasons.

• Set fit_nbinom to version 1.1: Version 1.0 Had deprecated function call of scipy > 1.2.

• Small documentation fixes and improvements.

April bug fix release

• Fixes KR balancing correction factors
• Deactivates log.debug

April release

The newest HiCExplorer release is the first release to support only Python 3, Python 2 support is discontinued. Release 3.0 brings the following features:

• Additional Hi-C interaction matrix correction algorithm 'Knight-Ruiz' as a C++ module for a faster run time and less memory usage.
• Enriched regions detection tool: 'hicDetectLoops' based on strict candidate selection, 'hicFindEnrichedContacts' was dropped.
• Metadata for cooler files is supported: hicBuildMatrix and hicInfo are using it
• New options for hicPlotMatrix: --loops to visualize computed loops from hicDetectLoops and --bigwigAdditionalVerticalAxis to display a bigwig track on the vertical axis too.
• Fixed a bug for applying correction factor on a matrix created by hic2cool version >= 0.5.

Early 2019 3rd bug fix

This bug fix release patches an issue with cooler files, hicBuildMatrix and the usage of a restriction sequence file instead of fixed bin size.

Early 2019 2nd bug fix

This bug fix release removes reference to hicExport that were forgotten to delete in 2.2. Thanks @BioGeek for this contribution.

Early 2019 bug fix

• Add option to write a file as output for hicInfo
• Muting log output from matplotlib and cooler
• Update dependency to hicmatrix 7 with corrected usage of cooler 0.8.2

Early 2019

We are happy to announce the release of HiCExplorer version 2.2.
Thanks for all the contributions: @LeilyR, @GinaRe, @gtrichard, @vivekbhr, @dpryan79, @bgruening, @Rungetf

This release contains many changes in the background especially how matrices are handled. The central class
'HiCMatrix' was moved to its own library: deeptools/HiCMatrix.
More matrix formats are supported (homer, hicpro, cool, h5), older formats are dropped (Lieberman, Dekker, npz, bing ren) and new functions (normalization, TAD averaging) were added.

HiCExplorer 2.2 will be the last release supporting Python 2.7.

A detailed list of changes:

• replaced hicExport by hicConvertFormat and hicAdjustMatrix
• extended functionality for hicConvertFormat:
  • read support for homer, hicpro, cool, h5
  • write support for h5, homer, cool
  • convert hic to cool
  • creation of mcool matrices
• hicAdjustMatrix:
  • remove, keep or mask specified regions from a file, or chromosomes
• hicNormalize:
  • normalize matrices to 0 - 1 range or to the read coverage of the lowest given
• hicBuildMatrix:
  • support for build mcool
• restructuring the central lass HiCMatrix to object oriented model and moved to its own library: deeptools/HiCMatrix.
  • Extended read / write support for file formats
  • better (faster, less memory) support for cool format
  • remove of old, unused code
  • restrict support to h5 and cool matrices, except hicConvertFormat
• hicPlotTADs: removed code and calls pyGenomeTracks
• hicAverageRegions: Sum up in a given range around defined reference points. Useful to detect changes in TAD structures between different samples.
• hicPlotAverageRegions: Plots such a average region
• hicTransform: Restructuring the source code, remove of option 'all' because it was generating confusion. Adding option 'exp_obs', exp_obs_norm and exp_obs_lieberman. These three different options use different expectation matrix computations.
• hicPCA:
  • Adding --norm option to compute the expected matrix in the way HOMER is doing it. Useful for drosophila genomes
  • Adding option to write out the intermediate matrices 'obs_exp' and 'pearson' which are necessary in the computation of the PCA
• hicPlotMatrix:
  • Add option to clip bigwig values
  • Add option to scale bigwig values
• Removed hicLog2Ration, functionality is covered by hicCompareMatrices
• Extending test cases to cover more source code and be hopefully more stable.
• Many small and big bugfixes
• Updating minimum requirements to:
  • numpy >= 1.15
  • scipy >= 1.1.
  • matplotlib >= 2.2
  • pysam >= 0.14
  • intervaltree == 2.1.
  • biopython >= 1.72
  • tables >= 3.4
  • pandas >= 0.23
  • pyBigWig >= 0.3
  • six >= 1.11
  • future >= 0.17
  • cooler >= 0.7.11
  • jinja2 >= 2.10
  • unidecode >= 1.0
  • hicmatrix >= 5
  • pygenometracks >= 2.1
  • scikit-learn >= 0.20
  • psutil >= 5.4.8

Beta release

The beta version of release 2.2 contains:

• replaced hicExport by hicConvertFormat and hicAdjustMatrix
• extended functionality for hicConvertFormat:
  • read support for homer, hicpro, cool, h5
  • write support for h5, homer, cool
  • convert hic to cool
  • creation of mcool matrices
• hicAdjustMatrix:
  • remove, keep or mask specified regions from a file, or chromosomes
• hicNormalize:
  • normalize matrices to 0 - 1 range or to the read coverage of the lowest given
• hicBuildMatrix:
  • support for build mcool
• restructuring the central lass HiCMatrix to object oriented model and moved to its own library: deeptools/HiCMatrix.
  • Extended read / write support for file formats
  • better (faster, less memory) support for cool format
  • remove of old, unused code
  • restrict support to h5 and cool matrices, except hicConvertFormat
• hicPlotTADs: removed code and calls pyGenomeTracks
• hicAverageRegions: Sum up in a given range around defined reference points. Useful to detect changes in TAD structures between different samples.
• hicPlotAverageRegions: Plots such a average region
• hicTransform: Restructuring the source code, remove of option 'all' because it was generating confusion. Adding option 'exp_obs', exp_obs_norm and exp_obs_lieberman. These three different options use different expectation matrix computations.
• hicPCA:
  • Adding --norm option to compute the expected matrix in the way HOMER is doing it. Useful for drosophila genomes
  • Adding option to write out the intermediate matrices 'obs_exp' and 'pearson' which are necessary in the computation of the PCA
• hicPlotMatrix:
  • Add option to clip bigwig values
  • Add option to scale bigwig values
• Removed hicLog2Ration, functionality is covered by hicCompareMatrices
• Extending test cases to cover more source code and be hopefully more stable.
• Many small and big bugfixes
• Updating minimum requirements to:
  • numpy >= 1.15
  • scipy >= 1.1.
  • matplotlib >= 2.2
  • pysam >= 0.14
  • intervaltree == 2.1.
  • biopython >= 1.72
  • tables >= 3.4
  • pandas >= 0.23
  • pyBigWig >= 0.3
  • six >= 1.11
  • future >= 0.17
  • cooler >= 0.7.11
  • jinja2 >= 2.10
  • unidecode >= 1.0
  • hicmatrix >= 5
  • pygenometracks >= 2.1
  • scikit-learn >= 0.20
  • psutil >= 5.4.8

2.1.4 bug fix release

This release fixes two bugs:

• cooler file format correction factors are applied as they should be
• parameter '--region' of hicBuildMatrix works with Python 3

2.1.3 bug fix release

The third bugfix release of version 2.1 corrects an error in hicPlotViewpoint. It adds a feature requested in issue #169 which should have been included in release 2.1 but was accidentally not.

From 2.1 release note:
hicPlotViewpoint: Adds a feature to plot multiple matrices in one image