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a package for orthogonal linear separation analysis (OLSA)

Project description

OLSApy


OLSApy: Orthogonal Linear Separation Analysis in Python


  • OLSA is an analysis method of omics data to decompose the complex effects of a perturbagen into basic components.
  • OLSApy is a package for OLSA in python.
  • OLSA can be applied to any kinds of omics data such as RNA-seq, proteome, and so on.

Dependency

  • python >= 3.6
  • requirements: numpy, pandas, scipy

Setup

pip install olsapy
For conda, please use conda skeleton


Usage

from olsapy import olsa

df = <a dataframe of interest (feature x sample)>

### calculation
dat = olsa.OLSA()
dat.load_df(df)
dat.olsa(accumulation=0.6) # accumulation determines the vectors subjected to varimax rotation
rsm,rvm,ts,contribution = dat.get_res()
### visualization
dat.plot(focus=[<sample names of interest>])

### visualization of already prepared data
dat.plot(rsm,focus=[<sample names of interest>])

Licence

This software is released under the MIT License, see LICENSE.


Authors

Setsuo Kinoshita, Shotaro Maedera, and Tadahaya Mizuno


References


Bug Report

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

Project details


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