├── .gitignore ├── LICENSE ├── README.md ├── Snakefile ├── conda_requirement.txt ├── config.yaml ├── docs ├── .buildinfo ├── .doctrees │ ├── environment.pickle │ └── index.doctree ├── Makefile ├── build │ ├── doctrees │ │ ├── docs.doctree │ │ ├── documentation.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── installation.doctree │ │ ├── manual.doctree │ │ └── quickstart.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ ├── bar_plot_affected_genes.png │ │ ├── distribution.gif │ │ ├── method.png │ │ └── snail_method.png │ │ ├── _sources │ │ ├── docs.rst.txt │ │ ├── documentation.rst.txt │ │ ├── index.rst.txt │ │ ├── installation.rst.txt │ │ ├── manual.rst.txt │ │ └── quickstart.rst.txt │ │ ├── _static │ │ ├── alabaster.css │ │ ├── bar_plot_affected_genes.png │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ └── theme.css │ │ ├── custom.css │ │ ├── distribution.gif │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Light.woff │ │ │ ├── Roboto-Slab-Light.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── Roboto-Slab-Thin.woff │ │ │ ├── Roboto-Slab-Thin.woff2 │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── method.png │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── snail_method.png │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── docs.html │ │ ├── documentation.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── manual.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── quickstart.html │ │ ├── search.html │ │ └── searchindex.js ├── make.bat ├── modules.rst ├── qsmooth.rst ├── setup.rst ├── source │ ├── _static │ │ ├── bar_plot_affected_genes.png │ │ ├── distribution.gif │ │ ├── method.png │ │ └── snail_method.png │ ├── conf.py │ ├── documentation.rst │ ├── index.rst │ ├── installation.rst │ ├── manual.rst │ └── quickstart.rst └── test.rst ├── pip_requirement.txt ├── pysnail ├── __init__.py ├── __main__.py ├── dataset.py ├── qsmooth.py └── utils.py ├── sample_data ├── expression.tsv ├── groups.tsv └── qsmooth.tsv ├── scripts ├── annotate_false_positives.py ├── comparison.py ├── compute_lioness.py ├── convert_gene_name.py ├── distribution_analysis.py ├── download_encode.R ├── download_gtex.sh ├── evaluation.py ├── lioness.R ├── memory_time_usage.py ├── normalize_expression.R ├── predict_gene_function.py ├── process_encode.py ├── process_gtex.py ├── run_different_threshold.sh └── utils.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kuijjerlab/PySNAIL/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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