yolish / hbm

hbm

Hierarchical block matrices (HBMs) are a powerful means for representing chromosome topology, which can be used to analyse high-throughput chromosome conformation capture (HiT-3C) data. This repository provides the implementation of three HBM-based algorithms: chromoHBM, chromoHBM-3D and chromoHBM-3C.

chromoHBM: an iterative algorithm for computing HBMs from chromosomal contact maps in order to compress them into topological features. chromoHBM-3D: an algorithm for guiding the 3D reconstruction of chromosomal structures using HBM traversal. chromoHBM-3C: an algorithm for merging HBMs as a means for integrating HiT-3C contact maps.

References Shavit, Y. Algorithms for reconstructing the 3D genome architecture. PhD thesis, October 2015.

hbm's Issues

Values of parameters in everystep

Hi,
I have read your great manuscript on Bioinformatics.
I'm very curious about the hierarchical TAD, but I can't get any output, since I don't know what to write in the parameters even at the start of the step ——'chromHBM'. What troubles me is the content that should writen into the partameter 'cluster_method' and 'cluster_argument', maybe as well as other parameters in the next two steps —— 'h1', 'h2' in 'chromoHBM-3D' and 'd', 'hbm.rep', 'method', 'argument' in 'chromHBM-3C'.

Thus, could you please provide me more details about meaning and possible values of the parameters in every steps? I think the README should be more practicable and user-friendly, which will let users use it without confusion.

Any reply will be helpful. Thanks a lot！