DiseaseCapsule

Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks

Installation and dependencies

No need to install the source code. Dependencies can be installed with a few minutes.

One could see pipeline.sh for the general workflow of analysis in this study.

Our proposed DiseaseCapsule:

Other approaches for comparison:

Potentially diease-related core genes and non-additive genes selection:

The ALS data used in this study has been deposited at dbGaP database (Accession: phs003146.v1.p1). Synthetic data can be seen here: https://drive.google.com/open?id=1Mya0YdT4Hf9wUfbcX6y5mubEFWky6Jg-

Name		Name	Last commit message	Last commit date
Latest commit History 13 Commits
.ipynb_checkpoints		.ipynb_checkpoints
data_preprocessing		data_preprocessing
figures		figures
.DS_Store		.DS_Store
CNN.GPU.py		CNN.GPU.py
LICENSE		LICENSE
MLP.GPU.py		MLP.GPU.py
README.md		README.md
basicML.py		basicML.py
basicML_allpca.py		basicML_allpca.py
capsule.GPU.py		capsule.GPU.py
classifier_PRS.py		classifier_PRS.py
pipeline.sh		pipeline.sh
select_core_genes_for_classification.ipynb		select_core_genes_for_classification.ipynb
select_nonadditive_genes.py		select_nonadditive_genes.py