{ "info": { "author": "Han Luo", "author_email": "hluo_lc@outlook.com", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "HiCHap\n******\nA Library of Hi-C data processing, bias correction and structural analysis for phased haplotype\n\nIntroduction\n============\nHiCHap is a Python package designed to process and analyze Hi-C data, primarily for diploid Hi-C by using phased SNPs. \nFirst, the Hi-C reads are split in ligation junction sites, and then all split parts are used in mapping to maximumly utilize SNPs in allele assignment, \nthus improving the ratios of allele-assigned reads. The noisy reads are further eliminated. Second, except for traditional data bias caused by Hi-C experiments, \nthe unevenly distributed genetic variants lead to additional bias in reconstructed Hi-C haplotype because it is potentially easier to assign allelic contacts in the chromatin regions with denser genetic variants. \nHiCHap utilizes a two-step strategy to reduce these two types of data biases by using the mapped and allele-assigned contacts only. \nThird, with the improved quality of reconstructed Hi-C haplotype, HiCHap can identify compartments, topological domains/boundaries and chromatin loops at haplotype level, \nand also provide testing on the allelic specificity for these structures. \nFinally, HiCHap supports data processing, bias correction and structural analysis for traditional Hi-C without separating homologous chromosomes.\n\n\nRequirements\n============\nHiCHap is developed and tested on Unix systems. HiCHap utilizes HDF5 and cooler as default data format to keep consistent with 4DN standards. \nTo summarize, the following packages are required in installation.\n\n\npython packages:\n\n1. Python 2.7+\n2. Multiprocess \n3. Numpy\n4. Scipy\n5. statsmodels\n6. Scikit-Learn\n7. xml\n8. pysam\n9. ghmm\n10. 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