omicexperiment 0.1.2.dev1
For analysis of omic experiments.
License: BSD
Keywords: bioinformatics

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