MLG

Machine Learning in Genomics Course ETH.

THE AMOEBAS

Moodle:

https://moodle-app2.let.ethz.ch/course/view.php?id=16540

Project server:

https://project.ml4g.ethz.ch/

Project 1 - Prediction of Gene Expression from Chromatin Landscape

Setup

Dependencies for conda and pip are listed in environment.yml and requirements.txt. In the project base folder execute in the command line:

conda env create -f environment.yml
pip install -r requirements.txt

Data

The project data should be unzipped into /task_1/data. For example, the X1 dataset train info should be available at /task_1/data/CAGE-train/X1_train_info.tsv.

We're using the human reference genome version hg38. It should be downloaded into the folder data from https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.

Dependencies

• Histone modification data processing with pyBigWig.