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Allen Lynch
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{ | ||
"cells": [ | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"# LISA: Landscape In-Silico deletion Analysis\n", | ||
"<hr>\n", | ||
"\n", | ||
"## About\n", | ||
"\n", | ||
"LISA predicts which TFs regulate a set of genes using integrative modeling of chromatin accessiblity and ChIP-seq binding. Particularly, LISA models the effects of deleting the influence of a TF on the expression of the genes-of-interest. For more information, see <a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1934-6>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1934-6</a>. This implementation extends the original, running 30x faster, reducing dependencies, and adding useful CLI functions for pipeline integration. " | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## Requirements\n", | ||
"\n", | ||
"* python >= 3.6\n", | ||
"* numpy, scipy, scikit-learn, and h5py\n", | ||
"* ~15GB of storage space" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## Installation\n", | ||
"\n", | ||
"LISA is available for install from PyPI. It is recommended that you set up a virtual environment using ```venv```, then run:" | ||
] | ||
} | ||
], | ||
"metadata": { | ||
"kernelspec": { | ||
"display_name": "lisa_test", | ||
"language": "python", | ||
"name": "lisa_test" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
"name": "ipython", | ||
"version": 3 | ||
}, | ||
"file_extension": ".py", | ||
"mimetype": "text/x-python", | ||
"name": "python", | ||
"nbconvert_exporter": "python", | ||
"pygments_lexer": "ipython3", | ||
"version": "3.7.3" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 4 | ||
} |
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'scikit-learn' | ||
], | ||
include_package_data=True, | ||
python_requires='>=3.6', | ||
) |