HiCExplorer Versions Save

• Fixing the wrong p-value computation in for chicViewpoint. New method is more accurate for floating points.
• Fixing a bug in chicViewpointBackgroundModel and chicQualityControl if an non-existing reference point was used.
• Improving all chic* modules with a capturing of errors in sub-processes. It is now guaranteed that the computation will terminate. Either successfull or by error.
• Add option 'truncateZero' to chicViewpointBackgroundModel: This removes all zero values for the distributions before fitting to fight over dispersion.
• Add option 'decimalPlaces' to chicViewpoint to adjust the decimal places in the output for all floating values. Helpful for really small p-values
• Add option 'truncateZeroPvalues' to chicSignificantInteractions to set all p-values which are 0 to 1 and are therefore ignored.
• Add option 'truncateZeroPvalues' to chicPlotViewpoint to set all p-values which are 0 to 1 and do not disturb the presentation of real p-values

• Improving the documentation
• hicPlotMatrix: add three options: change font size, change rotation of X label and change rotation of Y labels
• hicDetectLoops: add option to apply a parallelization within each chromosome
• hicPlotAverageRegions: Fixing the plotting. Thanks @lldelisle
• chic*-modules: change output from .bed to .txt

This release fixes a bug in chicViewpoint that caused a crash if the data to be averaged is less than the window size.

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

• Bug fix labels chicPlotViewpoint concerning the MB value range
• Add option to chicViewpoint to pre-compute an x-fold of value for the p-values per relative distance

• Fixing many bugs:
  • A bug in hicDetectLoops if a sub-matrix was very small
  • A bug in hicPlotMatrix if the region defined by --region was only a chromosome and loops should be plotted too
  • A bug in hicPlotMatrix if a loop region should be plotted and chromosomeOrder argument was used too
  • A bug in hicAggregateContacts (issue #405) if chromosomes were present in the matrix but not in the bed file
  • A bug in hicAdjustMatrix concerning a bed file and consecutive regions, see issue #343
  • A bug in hicAdjustMatrix if a chromosome is present in the matrix but not in the bed file, see issue #397
  • A bug in hicCompartmentsPolarization concerning the arguments 'quantile' and 'outliers' were interpreted as strings but should be integers
  • A bug in hicAdjustMatrix concerning the 'keep' option and how matrices are reordered internally. Thanks @LeilyR

Added features as requested:

• hicPCA ignores now masked bins, see issue #342

• chicPlotViewpoint:

  • Better legend handling on x-axis
  • Peaks are now display with their fill width
  • Add option --pValueSignificantLevels to categorize the p-values in x levels (e.g. 0.001 0.05 0.1)

• chicViewpoint:

  • adding sorting via viewpoints and not by samples option (--allViewpointsList)

• Adding an option to hicNormalize to normalize via multiplication and a user defined value (see issues #385, #424)

• Restructure source code of hicAdjustMatrix to have a better accessibility to its functions from outside of main

• Improving the documentation and fixing grammar / spelling mistakes. Thanks @simonbray

• New script: hicPlotSVL to investigate short range vs long range ratios.

• Adding the new captured Hi-C module. Viewpoint analysis based on a background model, significant interaction detection and differential analysis are provided. Thanks to @rgilsbach and @DonStephano .
• Adding documentation for captured Hi-C module and a tutorial on how to use it.
• Adding a module to be able to detect quite fast the quality of a Hi-C data set: hicQuickQC.
• Adding a tool to merge loops of different resolutions.
• Improving validation of locations: Presorting is no longer necessary; adding feature to add 'chr' prefix to loop or protein chromosome name
• Change loop detection slightly to improve results and fixed bugs:
  • preselection p-value was ignored and only p-value was used
  • adding additional test to the peak region test to decrease false discoveries
  • exchanging pThreshold / ln(distance) to remove too low values by a share of the maximum value of the distance. New parameter 'maximumInteractionPercentageThreshold'
• Removal of the folder 'scripts' and its content. These were outdated scripts and will maybe part of regular Hi-C tools in the future.

This new release updates HiCExplorer to version 3.1:

• Improved memory handling for hicCorrectMatrix with KR algorithm
• Adding a script to validate loop locations with protein peak locations
• Adding a script to compute the global compartmentalization signal
• Typos and documentation improvements.

• 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.

• Fixes KR balancing correction factors
• Deactivates log.debug