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@ay-lab ay-lab released this 21 Sep 07:07
· 131 commits to master since this release
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This release contains updated FitHiChIP code with the following changes, and corresponds to the manuscript published as BioRxiv:

  1. Added a new module for differential analysis of two categories of FitHiChIP loops, each with multiple replicates.
  2. Included a separate script for peak calling from the HiChIP data itself, for use in the significance estimation.
  3. Added various utility scripts for producing contact matrix of varying resolutions, merging ChIP-seq alignments, and generating ChIP-seq coverage of individual replicates. These files are all used for the proposed differential analysis.
  4. Minor bug fix in the merging adjacent loop code.
  5. Added functionality of plotting distance vs contact count for the significant loops.
  6. Discarded various redundant parameters from the configuration file and the code implementation.
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