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@joachimwolff joachimwolff released this 28 Jan 17:06
· 534 commits to master since this release
3.4
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Learn about vigilant mode.

Release 3.4 of HiCExplorer comes with improvements in the documentation and smaller bug fixes:

  • Fixing a bug in hicAdjustMatrix: keep option had a bug concerning the cutting before the end of a chromosome or the start position was not from the beginning of the chromosome
  • hicCompartmentPolarization was renamed to hicCompartmentalization and got some bug fixes:
    • set an offset to remove diagonals to help with the artifact they may generate
    • Removed the last quantile from the polarization calculation
    • sum devides by count at the end of the loop and only affects the final output
  • Extending the option on how the observed vs. Expected matrix is computed and adding the parameter --ligation_factor to achieve a rescale behaviour of the values as it is implemented in Homer. The same changes are applied to hicTransform
  • Improved the documentation
  • Adding an option in hicAverageRegions to select start, end, center or start_end as start index for up/downstream range.
  • hicBuildMatrix: Removed default value of binSize to enable mutually exclusive group error if not one of them is set. Behaviour so far was that the binSize was taken.
  • hicPlotSVL: adding xlegend to plot of SVL ratios to indicate the data points per boxplots are the chromosome ratios
  • hicQuickQC: Removed binSize option of hicQuickQC because it does not matter for QC calculation and adding a sentence to recommend the usage of restriction enzyme and dangling end sequence. Fixing bug issue #464
  • hicNormalize: Adding option in hicNormalize to remove values after the normalization if values are smaller than a given threshold
  • Capture Hi-C modules: Change background model distribution assumption from negative binomial to continuous negative binomial by using Gamma functions as a replacement for the binomial coefficient. Source: https://stats.stackexchange.com/questions/310676/continuous-generalization-of-the-negative-binomial-distribution/311927
  • hicInfo: Implementing feature request #456. The length of chromosomes is now show in the information too
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