Algorithms in Bioinformatics course project

Lovisa Franzén, [email protected]

Description

This is a project work for the Algorithms in Bioinformatics course organized by Lukas Käll.

All the code for this project was written in Python 3, and I used Jupyter Notebook to store my code and results. The notebook is called main_analysis.ipynb and is located in the results/ directory, along with an exported .html file generated of the notebook. It can also be viewed in nbviewer here: https://nbviewer.jupyter.org/github/lfranzen/algbio-course-project/blob/master/results/main_analysis.ipynb

A report containing a brief summary of the project outcome can be read in the report.pdf document located in the doc/ folder.

Environment

The conda environment that was used for this project ("abi_project") was exported as a yml file.
To install this environment, one can run:

$ conda env create -f environment.yml

To enable the environment in Jupyter Notebook one also needs to add:

$ python -m ipykernel install --user --name abi_project

Data

For this project I analysed a RNA-seq dataset that is publicly available at GEO with accession number GSE83888 (link), published by Barrette et al. in 2016.