not Just Another Biomarker
Project description
(not) Just Another Biomarker (nJAB)
njab
is a collection of some python function building on top of
pandas
, scikit-learn
, statsmodels
, pingoin
, numpy
and more...
It aims to provide a procedure for biomarker discovery which was first developed for a paper on fatty liver disease.
Installation
Install using pip from PyPi version.
pip install njab
or directly from github
pip install git+https://github.com/RasmussenLab/njab.git
Tutorials
The tutorial can be found on the documentation of the project with output or can be run directly in colab.
Explorative Analysis of survival dataset
The tutorial builds on a dataset example of survival of prostatic cancer.
The main steps in the tutorial are:
- Data loading and inspection
- Uncontrolled binary and t-tests for binary and continous variables respectively
- ANCOVA analysis controlling for age and weight, corrected for multiple testing
- Kaplan-Meier plots of for significant features
Biomarker discovery tutrial
All steps are describe in the tutorial, where you could load your own data with minor adaptions. The tutorial build on an curated Alzheimer dataset from omiclearn. See the Alzheimer Data section for more information.
The main steps in the tutorial are:
- Load and prepare data for machine learning
- Find a good set of features using cross validation
- Evaluate and inspect your model retrained on the entire training data
Documentation
Please find the documentation under njab.readthedocs.io
Project details
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