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Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods

Citation

If you use this repository, please cite our publication in Briefings in Bioinformatics : Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods

Problem

Compare feature extraction methods for binary classification of cancer types and subtypes using blood-based biomarkers.

Approach

Build a generic pipeline to run any biomarker dataset on multiple feature extraction methods and classification models

Type of data used

Pipeline

pipeline

The Feature Extraction Method comparison pipeline code is made available as an R package, inside the directory FEMPipeline.

To use this in your project :

devtools::install_github("abhivij/bloodbased-pancancer-diagnosis/FEMPipeline")

And within R :

library(FEMPipeline)

The function to call the pipeline is execute_pipeline.

To obtain information regarding the arguments, within R, use

?execute_pipeline

Main inputs to the pipeline are :

Code & Directory Structure

The R script files outside the FEMPipeline directory calls the FEMPipeline package for datasets relevant to this study