a package for orthogonal linear separation analysis (OLSA)
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.
- python >= 3.6
- requirements: numpy, pandas, scipy
pip install olsapy
For conda, please use conda skeleton
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>])
This software is released under the MIT License, see LICENSE.
Setsuo Kinoshita, Shotaro Maedera, and Tadahaya Mizuno
- Sci Rep. 2019 Feb 12;9(1):1824. doi: 10.1038/s41598-019-38528-4.
If you would like to report any bugs about olsapy, don't hesitate to create an issue on github here, or email me:
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