This package provides a function for RSS clasification. Paper:
To install the package, you can use pip:
pip install git+https://github.com/kisakol/RSS_Classifier.git
will be updated soon
Predicts the RSS clusters of the input data using the trained model and gene modules.
Args:
dataframe_path: The input data path. Rows should be samples and columns should be genes. First row should be the gene names (HUGO SYMBOLS). Data should be log2 transformed.
model_path: str: The path to the trained model.
modules_path: str: The path to the modules file.
scaled: bool: If the input data is scaled. Default is False.
output: str: The output file name. Default is "RSS_predictions".
Returns:
None
Writes:
A file with the predicted RSS clusters.
To use the function, simply import it and call it with the required arguments:
from rssclassifier.rssmodel import rss_predict
# Prepare input data
dataframe_path = "path/to/df"
# Call the function
rss_predict(dataframe_path, output="RSS_classifications")Kisakol, B., Matveeva, A., Salvucci, M. et al. Identification of unique rectal cancer-specific subtypes. Br J Cancer (2024). https://doi.org/10.1038/s41416-024-02656-0
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