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pyjugex

Travis (.com) PyPI Read the Docs (version)

Find a set of differentially expressed genes between two user defined volumes of interest based on JuBrain maps. The tool downloads expression values of user specified sets of genes from Allen Brain API. Then, it uses zscores to find which genes are expressed differentially between the user specified regions of interests. This tool is available as a Python package.

JuGEx homepage: http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html

repository: https://github.com/HumanBrainProject/PyJuGEx

Installation

Via pip:

pip install pyjugex

or from source

git clone https://github.com/HumanBrainProject/PyJuGEx
cd pyjugex
pip install -r requirements.txt
pip install .

Usage

see example usage

Dependencies

  • numpy
  • scipy
  • statsmodels
  • requests
  • nibabel
  • xmltodict

Versioning

1.0.1alpha

Authors

  • Big Data Analytics Group, INM-1, Research Center Juelich

Acknowledgments

  • Haimasree Bhattacharya
  • Dr. Sebastian Bludau, Dr. Thomas Mühleisen
  • Dr. Timo Dickscheid and other members of BDA-INM1

Reference

Sebastian Bludau, Thomas W. Mühleisen, Simon B. Eickhoff, Michael J. Hawrylycz, Sven Cichon, Katrin Amunts. Integration of transcriptomic and cytoarchitectonic data implicates a role for MAOA and TAC1 in the limbic-cortical network. 2018, Brain Structure and Function. https://doi.org/10.1007/s00429-018-1620-6