{ "info": { "author": "Jordan Berg", "author_email": "jordan.berg@biochem.utah.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# ![XPRESStools](https://raw.githubusercontent.com/XPRESSyourself/XPRESStools/master/docs/content/xpresstools.png)\n\n\n### A toolkit for navigating and analyzing gene expression datasets\n\n[![Build Status](https://travis-ci.org/XPRESSyourself/XPRESStools.svg?branch=master)](https://travis-ci.org/XPRESSyourself/XPRESStools)\n[![codecov.io](https://codecov.io/gh/XPRESSyourself/XPRESStools/XPRESStools.svg?branch=master)](https://codecov.io/gh/XPRESSyourself/XPRESStools)\n[![Documentation Status](https://readthedocs.org/projects/xpresstools/badge/?version=latest)](https://xpresstools.readthedocs.io/en/latest/?badge=latest)\n[![PyPi Status](https://img.shields.io/pypi/v/XPRESStools.svg)](https://pypi.org/project/XPRESStools/)\n[![DOI](https://zenodo.org/badge/170940002.svg)](https://zenodo.org/badge/latestdoi/170940002)\n\n##### Find documentation [here](https://xpresstools.readthedocs.io/en/latest/)\n\n-----\n\n### Development Notes:\nXPRESStools is still in beta production \nInteractive scatter plotting functions are not currently tested \nXPRESStools supports Python 2.7 and >=3.5 \n\n### Citation: \n```\nBerg, JA (2019). XPRESSyourself suite: Gene expression processing and analysis made easy. https://github.com/XPRESSyourself. DOI: 10.5281/zenodo.2581692.\n```\n\n### Installation: \n```\npip install xpresstools\n```\n\n### Other Requirements:\n- Tested on 64-bit Linux, compatible with Mac OS X\n- Python3 is recommended \n - Current test cases build to:\n - Python2.7\n - Python3.5\n - Python3.6\n - Python3.7\n- If [PyPi](https://pip.pypa.io/en/stable/installing/) and [Conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html?highlight=conda) are not already installed, these should be installed\n- If using this package to perform batch effect normalization or differential expression analysis, you must install [R](https://www.r-project.org/) \n- If using the interactive notebook provided, Jupyter needs to be [installed](https://jupyter.org/install) if not already\n\n### QuickStart: \nDownload the repository and modify the [interactive Jupyter notebook](https://github.com/XPRESSyourself/XPRESStools/blob/master/example_notebook.ipynb) to get started quick! \nRead the instructions as you navigate through the code blocks for a guide on how to use the example code \nCode blocks are run by selecting the block and pressing Shift + Enter \nSee [documentation](https://xpresstools.readthedocs.io/en/latest/) for more detailed instructions \n\n### Important Notes: \n* If working with XPRESStools within an interactive notebook (i.e. Jupyter Notebook, Atom Hydrogen, etc), you must include the following line of code after importing XPRESStools\n\n```\nimport XPRESStools as xp\n%matplotlib inline\n```\n\n* Assumes all dataframes are columns=samples and rows=genes (except in certain cases, see [documentation](https://xpresstools.readthedocs.io/en/latest/content/general-usage.html) for help) \n\n```\n>>> geo.head()\nname GSM523242 GSM523243 GSM523244 GSM523245 GSM523246 GSM523247 ... \n1007_s_at 8.98104 8.59941 8.25395 8.72981 8.70794 8.10693 ... \n1053_at 5.84313 6.59168 8.27881 6.64005 4.65107 7.19090 ... \n121_at 6.17189 5.73603 5.55673 5.69374 6.77618 5.84524 ... \n1294_at 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