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| include LICENSE.txt README.rst | ||
| include LICENSE.txt README.rst requirements.txt |
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| Welcome to GSEAPY's documentation! | ||
| ===================================================== | ||
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| GSEAPY: Gene Set Enrichment Analysis in Python. | ||
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| .. image:: https://badge.fury.io/py/gseapy.svg | ||
| :target: https://badge.fury.io/py/gseapy | ||
| .. image:: https://travis-ci.org/BioNinja/gseapy.svg?branch=master | ||
| :target: https://travis-ci.org/BioNinja/gseapy | ||
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| .. image:: https://img.shields.io/github/license/mashape/apistatus.svg | ||
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| GSEAPY is a python wrapper for **GESA**.It's used for convenient GO enrichments | ||
| and produce **publishable quality figures** from python. GSEAPY could be used for **RNA-seq, ChIP-seq, Microarry** data. | ||
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| `Gene Set Enrichment Analysis <http://software.broadinstitute.org/gsea/index.jsp>`_ (GSEA) | ||
| is a computational method that determines whether an a priori defined set of genes shows | ||
| statistically significant, concordant differences between two biological states (e.g. phenotypes). | ||
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| The full ``GSEA`` is far too extensive to describe here; see | ||
| `GSEA <http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page>`_ documentation for more information. | ||
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| Why GSEAPY | ||
| ----------------------------------------------------- | ||
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| For Gene Enrichment Analysis, ``GSEA`` is still the one of best choice. | ||
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| However, When you have large number of expression tables, or ``GO`` terms to enrich, ``GSEA`` desktop | ||
| version is inconvinient. What's more, the R version of GSEA has not been updated since 2006. | ||
| What's worse, ``GSEA`` desktop version do not provide means to modify plots, | ||
| like legends, ticks...... | ||
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| As a researcher of life science, I want a modern ``GSEA`` with lastest features. It can produce pubilishable | ||
| figures, and do many jobs at the same time without using mouse to select differrent data table, | ||
| differrent gene sets repeatly. | ||
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| Features of GSEAPY | ||
| ------------------------------------------------------ | ||
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| #. GSEAPY could reproduce the GSEA figures using GSEA desktop version results. | ||
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| #. GSEAPY could be used directly to perform enrichment anlysis. All parameters are same with ``GSEA`` | ||
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| #. GSEAPY is written in ``python``, using the same algorithm of ``GSEA`` Desktop version. | ||
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| #. GSEAPY produce figures in pdf format by default, which are ready for publishing and easy to modifiy. | ||
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| #. GSEAPY Enhancement will be considered. If you would like to contribute, please @BioNinja on ``Github``. | ||
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| GSEA desktop version output: | ||
| ------------------------------------------------- | ||
| This is an example of GSEA desktop application output | ||
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| .. figure:: GSEA_OCT4_KD.png | ||
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| GSEAPY output | ||
| ----------------------------------------------- | ||
| Using the same algorithm by ``GSEA``, GSEAPY reproduce the example above. | ||
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| .. figure:: gseapy_OCT4_KD.png | ||
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| Generated by GSEAPY | ||
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| **GSEAPY figures are PDF formats by default.** Other matplotlib figures formats are supported, too. | ||
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| You can modify ``GSEA`` plots easily in .pdf files. Please Enjoy. | ||
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| Installation | ||
| ---------------- | ||
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| | Install gseapy package from pypi and download | ||
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| .. code:: bash | ||
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| $ pip install gseapy | ||
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| | You may instead want to use the development version from Github, by running | ||
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| .. code:: bash | ||
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| $ pip install git+git://github.com/BioNinja/gseapy.git#egg=gseapy | ||
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| Dependency | ||
| -------------- | ||
| * Python 2.7 or 3.3+ | ||
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| Mandatory | ||
| ~~~~~~~~~~~~~~~~ | ||
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| * Numpy | ||
| * Pandas | ||
| * Matplotlib | ||
| * Beautifulsoup4 | ||
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| You may also need **lxml, html5lib**, if you could not parse xml files. | ||
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| Run GSEAPY | ||
| ----------------- | ||
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| | GSEAPY has two subcommands: ``replot``, ``call``. | ||
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| | The ``replot`` command will parse the GSEA desktop results directory(the path contains edb file folder). | ||
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| | The ``call`` command will compute es,nes,pval,fdr and generates plots, *de novo*. | ||
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| | For more information to use this library,see the :ref:`run`. |
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