Examples

Warning

If you want to run the examples, make sure you execute them in a directory where you have write permissions, or you copy the examples into such a directory. If you install biolean manually, make sure you have followed the instructions.

Omics Biomarker Examples

Plots results of running omics based biomarker models functions. Includes methylation and transcriptomic data.

Local Data Loading

Local Data Loading

“Transcriptomic Clock” using GEO Data

"Transcriptomic Clock" using GEO Data

“Epigenetic Clocks” in GEO Data

"Epigenetic Clocks" in GEO Data

Down Syndrome Epigenetic Plotting

Down Syndrome Epigenetic Plotting

Proteomic Organ Age Clock

Proteomic Organ Age Clock

Performing custom imputations

Performing custom imputations

Composite Biomarkers Examples

Plot survival curves based on clocks using data from standard blood tests

“Phenotypic Ages” in NHANES Data

"Phenotypic Ages" in NHANES Data

Challenge Submission Examples

Generate submissions for the biomarkers of aging challenge

Building a competition submission using an existing model

Building a competition submission using an existing model

Exploring the Challenge Data

Exploring the Challenge Data

Training an ElasticNet model

Training an ElasticNet model

Deconvolution Examples

Plots results of running deconvolution on dataset with known cell proportions

“Deconvolution Example”

"Deconvolution Example"

Additional Visualization Examples

This document showcases functions in visualize.py for visualizing quality control results, DNA methylation, and aging clock/model predictions

Quality control visualization using GEO datasets

Quality control visualization using GEO datasets

Clock/model visualizations using GEO datasets

Clock/model visualizations using GEO datasets

DNA methylation visualizations using GEO datasets

DNA methylation visualizations using GEO datasets