In these tutorials, we used NEASE in multiple datasets from both healthy and disease cohorts to study the functional impact of alternative splicing. Each notebook covers a single dataset.
To install the package from PyPI please run:
pip install nease
To install the package from git:
git clone https://github.com/louadi/NEASE.git && cd NEASE
pip install .
If you would like to run the tutorial jupyter notebooks, you need to install jupyter.
pip install jupyterlab
For VastDB analysis, you will also need:
pip install seaborn
and
pip install -U scikit-learn
Download and extract the files into AS data/VastDB
https://zenodo.org/record/5093528/files/vastdb.tar.xz?download=1
Or from VastDB website:
https://vastdb.crg.eu/wiki/Downloads
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VastDB analysis: Neural-specific exons (Notebook/Google Colab) Muscles-specific exons (Notebook/Google Colab)
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Dilated Cardiomyopathy analysis (An example for running NEASE on a standard input): (Notebook/Google Colab)
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Multiple Sclerosis analysis: (Notebook/Google Colab)
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Platelet analysis: (Notebook/Google Colab)
If you use NEASE, please cite:
Louadi, Z., Elkjaer, M.L., Klug, M. et al. Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biol 22, 327 (2021). https://doi.org/10.1186/s13059-021-02538-1