Metadata-Version: 2.1
Name: hiconet
Version: 0.5.1
Summary: Hierachical Community Network, data driven omics integration
Home-page: https://github.com/shuzhao-li/hiconet
Author: Shuzhao Li
Author-email: shuzhao.li@gmail.com
License: BSD
Description: # Hieracrchical Community Network
        for integration of multiple data types collected from a common group of subjects.
        
        ## Terminology:
            Study: Same as ImmPort "Study"
        
            Project: a collection of data of one or more types. For multiple data types, common samples/subjects are expected.
                This is the unit HiCoNet works on - HiCoNet integrates DataMatrices within a DataSet
                A DataSet should have at least one Society of data
        
        
            Society: one data type
            at least one of each DataMatrix, FeatureAnnotation, ObservationAnnotation
        
            DataMatrix: a data matrix of continuous values that represent a biological state or concentration, of the same data type.
                This can include different time points or treatments.
                This is the unit community detection is based on.
        
            ObservationAnnotation: meta data on samples. This may include TimePoints and Treatments, often in biosample table from ImmPort DB
            FeatureAnnotation: meta data on features
        
            Key annotation variables: time point and treatment.
            TimePoint:
            Treatment:
        
        
            Graph: a graph/network for relationships in the data (e.g. used in loom format, loompy.org).
            Community: a group of features within a society that share a similar pattern.
        
        
        
            Reusing
            -------
            The data structure is aligned with anndata (https://github.com/theislab/anndata) but transposed.
            For future consideration, e.g. in loom format, one loom file = a Society; as meta data can differ for different data types.
            Same goes for anndata.
        
        
        ## requires
            'PyYAML'
            'numpy',
            'scipy',
            'pandas',
            'sklearn',
            'leidenalg',
            'scanpy',
            'igraph',
            'fuzzywuzzy',
        
            Note: python-igraph requires the C library igraph  
            https://stackoverflow.com/questions/45667147/install-python-igraph-on-mac
            I did pip3 install ~/Downloads/python-igraph-0.7.1-1.tar.gz
            For a Docker or new install, both igraph and python-igraph are needed.
        
        
        ## Test run
        hiconet python3 -m hiconet.HiCoNet hiconet/datasets/SDY80
        
Keywords: bioinformatics systems biology immunology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/markdown
