Metadata-Version: 2.1
Name: TADLib
Version: 0.4.4
Summary: A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
Home-page: https://github.com/XiaoTaoWang/TADLib/
Author: XiaoTao Wang
Author-email: wangxiaotao686@gmail.com
License: UNKNOWN
Description: .. note:: Since version 0.4.0, the default data format has changed to `cool <https://github.com/mirnylab/cooler>`_,
           to comply with 4DN standards.
        
        
        Introduction
        ============
        Chromosome conformation capture (3C) derived techniques, especially Hi-C, have
        revealed that topologically associating domain (TAD) is a structural basis for
        both chromatin organization and biological functions in three-dimensional (3D)
        space. TAD is also hierarchically organized by smaller structural units, which
        are relevant to biological functions. To systematically investigate the relationship
        between structure and function, it is important to develop quantitative methods to
        identify and measure the organization of TAD. TADLib is such a library to explore
        the chromatin interaction patterns inside TAD from Hi-C chromatin interactions.
        
        Currently, TADLib consists of two methods:
        
        - Aggregation Preference (AP)
            AP is a quantitative parameter to measure the overall density of significant
            chromatin interactions inside TAD. Inspired by the observation that there exist
            great differences in chromatin interaction pattern among TADs, an empirical
            parameter called Aggregation Preference (AP) can be used to capture these
            aggregation degree of significant chromatin interactions. Application to human
            and mouse cell types (including both traditional Hi-C and in situ Hi-C data sets)
            shows that there exist heterogeneous structures among TADs and the structural
            rearrangement across cell types is significantly associated with transcriptional
            remodelling. [1]_
        - Hierarchical TAD (HiTAD)
            HiTAD is a method to detect hierarchical TADs, including TADs, sub-TADs and
            smaller domains. Except local insulations, HiTAD further constrains TADs as the
            optimal domains to globally separate intra-chromosomal interactions. Under
            objective functions derived from chromatin interactions, HiTAD adopts an iterative
            optimization procedure to detect hierarchical TADs. HiTAD performs well in domain
            sensitivity, replicate reproducibility and inter cell-type conservation. Application
            to human and mouse cell types (including both traditional Hi-C and in situ Hi-C data
            sets) reveals that there exist common change types for hierarchical TADs, which are
            involved in shaping higher-order compartment, replication timing and transcriptional
            regulation. [2]_
            
        
        Links
        =====
        - `Detailed Documentation <https://xiaotaowang.github.io/TADLib/>`_
            - `Installation <https://xiaotaowang.github.io/TADLib/install.html>`_
            - `Aggregation Preference <https://xiaotaowang.github.io/TADLib/calfea.html>`_
            - `Hierarchical TAD <https://xiaotaowang.github.io/TADLib/hitad.html>`_
            - `Detect Single-level TAD <https://xiaotaowang.github.io/TADLib/domaincaller.html>`_
            - `Visualization <https://xiaotaowang.github.io/TADLib/visualize.html>`_
        - `Code Repository <https://github.com/XiaoTaoWang/TADLib>`_ (At GitHub, Track the package issue)
        - `PyPI <https://pypi.python.org/pypi/TADLib>`_ (Download and Installation)
        	
        Citation
        ========
        .. [1] Wang XT, Dong PF, Zhang HY, Peng C. Structural heterogeneity and functional diversity
           of topologically associating domains in mammalian genomes. Nucleic Acids Research, 2015,
           doi: 10.1093/nar/gkv684
        
        .. [2] Wang XT, Cui W, Peng C. HiTAD: detecting the structural and functional hierarchies of
           topologically associating domains from chromatin interactions. Nucleic Acids Research, 2017,
           doi: 10.1093/nar/gkx735
        
Keywords: TAD Aggregation Preference AP sub-TAD hierarchy Hi-C cooler
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: POSIX
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
