Pre-release

@joachimwolff joachimwolff released this Nov 23, 2018 · 44 commits to release22beta since this release

Assets 2

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

@joachimwolff joachimwolff released this May 25, 2018 · 3 commits to master since this release

Assets 2

This release fixes two bugs:

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

@joachimwolff joachimwolff released this May 7, 2018 · 9 commits to master since this release

Assets 2

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

@joachimwolff joachimwolff released this Apr 26, 2018 · 18 commits to master since this release

Assets 2

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.

@fidelram fidelram released this Mar 27, 2018 · 47 commits to master since this release

Assets 2

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

@joachimwolff joachimwolff released this Mar 5, 2018 · 55 commits to master since this release

Assets 2

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
Pre-release
Pre-release

@joachimwolff joachimwolff released this Feb 27, 2018

Assets 2

This pre-release contains:

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

@joachimwolff joachimwolff released this Dec 28, 2017 · 193 commits to master since this release

Assets 2

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
Assets 2

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

Assets 2

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