HBP specifications


Unique identifier OMICS_14354
Name Hi-C BED file analysis Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Hi-C raw datasets, interaction matrix files from hiclib or HiC-Pro, tracks files of histone modification or transcription factors DNA binding motif enrichment information of ChIP-seq.
Output data Interaction frequency distribution, network topology information, global scatter diagram, circus pictures with different tracks, network clusters according to these tracks, topological structure of the global genome and statistical evaluation, distribution of interactions between specific genome sites with their frequency.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.0
Stability Stable
Requirements optparse, grid, lattice, IDPmisc, OmicCircos, stringr, ggplot2, igraph, reshape2, pgirmess, coin, multcomp, flexclust, HiTC, rtracklayer, gplots
Maintained Yes



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  • person_outline Zhihu Zhao <>

HBP article

HBP institution(s)
Beijing Institute of Biotechnology, Beijing, China
HBP funding source(s)
This work was supported by National Basic Research Program of China [2013CB966802], National Natural Science Foundation of China [31370762, 31030026, 31272416, 81372218] and National Key Technology R&D Program of China [2012BAI01B07].

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