Metadata-Version: 1.2
Name: plastid
Version: 0.5.1
Summary: Tools for analysis of genomics & sequencing data
Home-page: https://github.com/joshuagryphon/plastid
Author: Joshua Griffin Dunn
Author-email: joshua.g.dunn@gmail.com
Maintainer: Joshua Griffin Dunn
Maintainer-email: joshua.g.dunn@gmail.com
License: BSD 3-Clause
Download-URL: https://pypi.python.org/pypi/plastid/
Description: Welcome to `plastid`!
        =====================
        
        For documentation, see `our home page
        <http://plastid.readthedocs.io/en/latest/>`_ on `ReadtheDocs
        <http://readthedocs.io>`_.
        
        To run the tests, download the `test dataset
        <https://www.dropbox.com/s/h17go7tnas4hpby/plastid_test_data.tar.bz2?dl=0>`_
        and unpack it into ``plastid/test``.
        
        
        Introduction
        ------------
        
        ``plastid`` is a Python library for genomic analysis -- in particular,
        high-throughput sequencing data -- with an emphasis on simplicity for users. It
        was written by Joshua Dunn in `Jonathan Weissman's lab
        <http://weissmanlab.ucsf.edu>`_ at `UCSF <http://ucsf.edu>`_,  initially for
        analysis of ribosome profiling and RNA-seq data. Versions of it have been used
        in several publications.
        
        ``plastid``'s intended audience includes computational and traditional
        biologists, software developers, and even those who are new to sequencing
        analysis. It is released under the BSD 3-Clause license.
        
        This package provides:
        
        #. A set of scripts that implement common sequencing analyses
        
        #. A set of classes for exploratory data anlysis. These provide simple
           and consistent interfaces for manipulating genomic features,
           read alignments, and quantitative data; and readily interface with
           existing scientific tools, like the SciPy stack.
        
        #. Script writing tools that make it easy to use the objects implemented in
           ``plastid``.
        
        #. Extensive documentation, both in source code and at `our home page
           <http://plastid.readthedocs.io/en/latest/>`_ on `ReadtheDocs
           <http://readthedocs.io>`_.
        
        
        Installation
        ------------
        
        Bioconda
        ........
        
        .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
           :target: http://bioconda.github.io/recipes/plastid/README.html
           :alt: install with bioconda
        
        ``Bioconda`` is a channel for the conda package manager with a focus on
        bioinformatics software. Once you have ``Bioconda`` installed, installing
        ``plastid`` is as easy as running::
        
            $ conda create -n plastid plastid
            $ source activate plastid
        
        This will install all of the necesary dependencies for ``plastid`` in an
        isolated environment.
        
        PyPI
        ....
        
        ``plastid`` can be installed directly from PyPI, but requires numpy, pysam,
        and cython to be installed first i.e.::
        
            $ pip install numpy pysam cython
            $ pip install plastid
        
        If you get any runtime warnings about numpy versions having changed, or about
        a missing module in Pysam, or about some object being the wrong size, try
        regenerating the included C source files from the original Cython code. To
        do this type::
        
            $ pip install --upgrade  --install-option='--recythonize' plastid
        
        
        Links & help
        ------------
        
        - `Documentation <http://plastid.readthedocs.io>`_
        
        - `Our github repo <https://github.com/joshuagryphon/plastid>`_
        
        - Subscribe to our mailing list by emailing ``listserv@listserv.ucsf.edu``
          with the message *subscribe plastidinfo firstname lastname* and an empty
          subject line
        
        - `Test dataset <https://www.dropbox.com/s/h17go7tnas4hpby/plastid_test_data.tar.bz2?dl=0>`_,
          for development or validation of installations
        
        - `Bioconda <bioconda.github.io>`_
        
Keywords: ribosome profiling riboseq rna-seq sequencing genomics biology
Platform: OS Independent
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Natural Language :: English
