Metadata-Version: 1.1
Name: omicexperiment
Version: 0.1.2.dev1
Summary: For analysis of omic experiments.
Home-page: https://github.com/bassio/omicexperiment
Author: Ahmed Bassiouni
Author-email: ahmedbassi@gmail.com
License: BSD
Download-URL: https://github.com/bassio/omicexperiment/tarball/0.1.2-dev1
Description: The *omicexperiment* python package
        ===================================
        
        The omicexperiment package is an open-source, BSD-licensed, Python 3
        package for analysis of dataframes of 'omic experiments', built upon the
        solid foundations of the Python scientific stack.
        
        The omicexperiment package has the goal of providing a pleasant API for
        *rapid* analysis of 'omic experiments' in interactive environments.
        
        The R bioinformatics community has already provided similar
        implementations for similar functionality. Examples include DESeqDataSet
        (from the package DeSeq2), MRExperiment (from the package
        metagenomeSeq), phyloseq-class (from the package phyloseq). To my
        knowledge, there exists no similar powerful functionality available to
        users of python.
        
        The philosophy of this package is to build upon solid foundations of the
        python scientific stack and try not to re-invent the wheel. Packages
        such as numpy and pandas are powerful optimized libraries in dealing
        with matrix and tabular data, respectively. This package's backend thus
        consists almost entirely of pandas DataFrames and pandas APIs.
        
        Example code
        ------------
        
        ::
        
            from omicexperiment.experiment.microbiome import MicrobiomeExperiment
            from omicexperiment.filters import Sample, Taxonomy
        
            mapping = "example_map.tsv"
            biom = "example_fungal.biom"
            tax = "blast_tax_assignments.txt"
        
            #our Experiment object
            exp = MicrobiomeExperiment(biom, mapping,tax)
        
            #include only samples with more than 90000 counts
            exp.filter(Sample.count > 90000)
        
            ##collapse the OTUs in the _data_ DataFrame to genus level assignment
            exp.filter(Taxonomy.groupby('genus')) #any taxonomic rank can be passed
        
        Installation
        ------------
        
        Just clone the git repository. Hopefully very shortly, the package will
        be uploaded to PyPi and will be pip-installable.
        
        Due to bugs in handling numpy installation in setuptools, it is better
        to install numpy first using 'pip install numpy'.
        
        Dependencies
        ------------
        
        Current omicexperiment dependencies:
        
        -  numpy
        -  scipy
        -  pandas
        -  scikit-bio
        -  biom-format
        -  lxml
        -  pygal
        
        License
        -------
        
        This package is released as open-source, under a BSD License. Please see
        COPYING.txt.
        
        Documentation
        -------------
        
        Please see the doc folder in the package
        (https://github.com/bassio/omicexperiment/tree/master/doc), it contains
        Jupyter notebooks that runs you through most of the current package
        functionality.
        
        Acknowledgements
        ----------------
        
        Thank you to all the great python bioinformatics and data science
        community for releasing their code as open source.
        
        Contributing and use in your research
        -------------------------------------
        
        Please be advised that at this stage, this package is still alpha
        software. Testing is still not implemented so be careful. But if you are
        interested in contributing to this project, please contact. Contributors
        are welcome to improve the software. Nowadays, I expect the package to
        continue growing slowly as I add functionality and improvements as long
        as I need it in my own research. I will be initially focusing on
        developing the MicrobiomeExperiment part.
        
        0.1.2-dev
        ---------
        
        -  Development version(s) dedicated to fixing PyPI installation.
        
        0.1.1
        -----
        
        -  Initial version
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
