Release History

1.5 (2017-08-15)

  • Updated quasar to final version

1.4 (2017-06-28)

  • Added conversion scripts for butlr and cooler heatmp formats
  • Added perliminary QuASAR scripts
  • Added support for matrix output in text and npz formats
  • Added hdf5 feature loading for fend files
  • Added boundary index and comportment likelihood scoring

1.3 (2016-04-28)

  • Added support for creating non-restriction enzyme-based HiC genome partitions
  • Added ability to load RE HiC data into binned genome partition
  • Added ability to directly load pre-binned matrix files
  • Added support for normalization and plotting of binned HiC data
  • Added matrix output option in hic-interval subcommand
  • Fixed error in sub-binning cis heatmap arrays
  • Compiled domain calling approaches into new hic_domain module
  • Renamed _hic_tads to _hic_domains in libraries
  • Removed ununsed functions in _hic_domains
  • Added explicit variable casting for compatibility with cythoning in Windows

1.2.2 (2015-12-15)

  • Added modified arrowhead transformation domain calling
  • Re-implemented modified version of boundary-index domain finding
  • Added cis sub-region binning function (no longer needs to extend to the diagonal)

1.2 (2015-10-21)

  • Added detailed statistics for loaded HiC data
  • Added testing of various data import functions
  • Added option to skip PCR duplicate filtering
  • Cleaned up HiC cis binning
  • Various bug fixes

1.1 (2015-08-26)

  • Added multi-resolution heatmaps (MRH).
  • Added stand-alone script for plotting MRH data.
  • Fixed requirements resolution for pip loading without requirements already installed.
  • Re-implemented Poisson model for HiC probability algorithm.
  • Lowered memory requirement for HiC data loading.
  • Added dockerfile for building docker image.

1.0.3 (2015-04-23)

  • Expanded functionality of Express to include support to Knight-Ruiz algorithm to both 5C and HiC algorthims.
  • Added binary counts option to Express in HiC.
  • Added non-logged counts functionality to Express in 5C.
  • Added pseudo-count option to Binning in HiC.
  • Dramatically sped up heatmap creation for ‘fend’-corrected heatmaps using probability or express corrections.
  • Added binary distance-dependence calculation alongside standard.

1.0.2 (2015-04-16)

  • Fixed Express algorithm stopping criteria.
  • Updated Probability algorithm and documentation.
  • Fixed bug introduced into HiC binning algorithm.
  • Added binning documentation.
  • Added Travis automated testing.