Metadata-Version: 2.1
Name: quasinet
Version: 0.0.34
Summary: Utitilies for constructing and manipulating models for non-local structural dependencies in genomic sequences
Home-page: https://github.com/zeroknowledgediscovery/
Author: zed.uchicago.edu
Author-email: ishanu@uchicago.edu
License: LICENSE.txt
Download-URL: https://github.com/zeroknowledgediscovery/quasinet/archive/0.0.34.tar.gz
Description: ===============
        quasinet
        ===============
        
        .. figure:: https://img.shields.io/pypi/dm/quasinet.svg
           :alt: quasinet PyPI Downloads
        
        .. figure:: https://badge.fury.io/py/quasinet.svg
           :alt: ehrzero PyPI Downloads
        
        .. image:: http://zed.uchicago.edu/logo/logozed1.png
           :height: 400px
           :scale: 50 %
           :alt: alternate text
           :align: center
        
        
        .. class:: no-web no-pdf
        
        :Author: ZeD@UChicago <zed.uchicago.edu>
        :Description: Infer Non-local Structural Dependencies In Genomic Sequences. Genomic sequences are esentially compressed encodings of phenotypic information. This package provides a novel set of tools to extract long-range structural dependencies in genotypic data that define the phenotypic outcomes. The key capabilities implemented here are as follows: 1. computing the q-net given a databse of nucleic acid sequences, which is a family of conditional inference trees capturing the predictability of each nucleotide position given the rest of the genome. 2. Computing a structure-aware evolution-adaptive notion of distance between genomes, which demonstrably is much more biologically relevant compared to the standard edit distance 3. Ability to draw samples in-silico, that have a high probability of being biologically correct. For example, given a database of HIV sequences, we can generate a new genomic sequence, which has a high probability of being a valid encoding of a HIV virion. The constructed q-net for long term non-progressor clinical phenotype in HIV-1 infection is shown below.
        
        
        .. image:: https://zed.uchicago.edu/data/img/q-ltnr.png
           :height: 400px
           :scale: 50 %
           :alt: q-net for long term non-progressor clinical phenotype in HIV-1 infection
           :align: center
        
        **Introduction:**
           
Keywords: decision,trees
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Requires-Python: ==2.7.*
Description-Content-Type: text/x-rst
