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

• Sci Rep. 2019 Feb 12;9(1):1824. doi: 10.1038/s41598-019-38528-4.
• http://www.ilincs.org/ilincs/

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:

• tadahaya@gmail.com
• tadahaya@mol.f.u-tokyo.ac.jp