PyROTS: Reproducibility-Optimized Test Statistic (in Python)

This is a Python wrapper for the ROTS R package which implements the Reproducibility-Optimized Test Statistic for differential testing in omics data. This means that while this package is run entirely in Python, underneath it runs an R process and the original R package. You do not need to care about all this, but you DO need to have R and the ROTS package installed.

You can install R from the R Project website: https://cran.r-project.org/. After that, run the following in terminal to install ROTS

Rscript -e 'if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("ROTS")'

Usage

Below is a minimal example that shows what the inputs should look like: data should be given as a pandas Data Frame and the group labels as a pandas Series. Samples are in columns and the order should match with groups.

import numpy as np
import pandas as pd
from PyROTS import ROTS

data = pd.DataFrame(np.random.normal(size = (100,10)), index = ["gene_" + s for s in list(map(str,range(100)))])
groups = pd.Series(5*["A"]+5*["B"])
res = ROTS(data, groups)

Please consult the documentation for the R package for details about the method and functionality.

NB: This is a work in progress, some functions might not be available.