Integrated Bioinformatics Project 2022

Characterization of Alzheimer's Disease using SCENIC+

A short description of the project

Create a new conda environment using the requirements file from root

conda create --name ibp-2022-env --file requirements.txt

If the creation was successful, you can check if the environment was created using

conda env list

If "ibp-2022-env" is listed in your available environments, simply activate the environment and download the additional scenic+ package from github.

conda activate ibp-2022-env

pip install git+https://github.com/aertslab/scenicplus.git

If you are using Jupyter Notebooks to run the code, you will need to create a kernel from your conda environment.

python -m ipykernel install --user --name=ibp-2022-env

Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
.gitignore		.gitignore
Glial SCENIC+ Gene Inference.ipynb		Glial SCENIC+ Gene Inference.ipynb
Glial SCENIC+.ipynb		Glial SCENIC+.ipynb
ODC SCENIC+.ipynb		ODC SCENIC+.ipynb
ODC SCENIC+Original.ipynb		ODC SCENIC+Original.ipynb
README.md		README.md
RegulonMG.ipynb		RegulonMG.ipynb
SCENIC+ Gene Inference.ipynb		SCENIC+ Gene Inference.ipynb
SCENIC+ ODC V2 Gene Inference.ipynb		SCENIC+ ODC V2 Gene Inference.ipynb
SCENIC+ V2 Gene Inference.ipynb		SCENIC+ V2 Gene Inference.ipynb
SCENIC+ V3 Gene Inference.ipynb		SCENIC+ V3 Gene Inference.ipynb
SCENIC+.ipynb		SCENIC+.ipynb
eRregulons_AD.ipynb		eRregulons_AD.ipynb
requirements.txt		requirements.txt
scRNA-seq-AD.ipynb		scRNA-seq-AD.ipynb