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a package for Decomposition of Profile Data

Project description

depro

a package for Decomposition profile data analysis to grasp the effects of small compounds.

Dependency

  • python 3.6
  • requirements: numpy, pandas, scipy, tqdm, enan

Setup

pip install depro

  • for conda environment, please use skeleton

Usage

see samplecode.ipynb

Licence

This software is released under the MIT License.

Authors

MIZUNO Tadahaya

References

This package is inspired from the following brilliant databases and studies:

  • Nat Genet. 2003 Jul;34(3):267-73.
  • PNAS. October 25, 2005 102 (43) 15545-15550.
  • BMC Bioinformatics. 2013;128(14).
  • Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377 .
  • Science. 2006 Sep 29;313(5795):1929-35.
  • MsigDB
  • EnrichR
  • CMap
    Also our results:
  • Development of Orthogonal Linear Separation Analysis (OLSA) to Decompose Drug Effects into Basic Components. Mizuno T, Kinoshita S, Ito T, Maedera S, Kusuhara H., Sci Rep. 2019 Feb 12;9(1):1824. doi: 10.1038/s41598-019-38528-4.

Bug Report

If you would like to report any bugs about this package, don't hesitate to create an issue on github here, or email me:

To Do

  • prepare sample code

Project details


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Files for depro, version 0.0.11
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