Oligo pipeline

This repository contains resources and code to run the pipeline as described in our article.

Required data format for the pipeline

The pipeline only accepts a (Pandas) dataframe with the following requirements/format:

sample_ID	compound	sample_amt	peak_area	creatinine_mmol_liter	age_in_years
Sample_1	904_α-mann	25	15000	1.5	2.2
..	..	..	..	..	..
Sample_n	1071_GM1	35	25000	2.1	10.1

where sample_amt is the semi-quantitative concentration of the compound, and peak_area is the area under the chromatographic peak.

A test notebook can be found in this repository on how to use the pipeline (see Pipeline_test.ipynb)