.gitignore
CHANGES
LICENSE
MANIFEST.in
README.md
mkdocs.yml
sample_config.json
setup.py
docs/index.md
docs_rst/advanced-usage.rst
docs_rst/conf.py
docs_rst/config.rst
docs_rst/custom-pdf.rst
docs_rst/custom.rst
docs_rst/help.rst
docs_rst/index.rst
docs_rst/install.rst
docs_rst/introduction.rst
docs_rst/license.rst
docs_rst/output-pdf.rst
docs_rst/output.rst
docs_rst/parameter.rst
docs_rst/uropa-example-pdf.rst
docs_rst/uropa-example.rst
docs_rst/uropa_gui.rst
docs_rst/img/Thumbs.db
docs_rst/img/chr1-1,403,500-1,408,500-01_h3k4me1_peaks.png
docs_rst/img/chr22-18161287-18161496_peak71_h3k4me1_feature_pos.png
docs_rst/img/chr6-27,857,165-27,863,637_internal_feature-01.png
docs_rst/img/config.png
docs_rst/img/custom.png
docs_rst/img/output-formats-summary.png
docs_rst/img/output1-2.png
docs_rst/img/output3-5.png
docs_rst/img/output6.png
docs_rst/img/peak_Upstream_Downstream_of_gene.png
docs_rst/img/uropa-example-tab1-4.png
docs_rst/img/uropa-example-tab5-6.png
test_data/gencode.v29.annotation.chr19.gtf
test_data/genomic_regions.bed
uropa/__init__.py
uropa/annotation.py
uropa/uropa.py
uropa/utils.py
uropa.egg-info/PKG-INFO
uropa.egg-info/SOURCES.txt
uropa.egg-info/dependency_links.txt
uropa.egg-info/entry_points.txt
uropa.egg-info/not-zip-safe
uropa.egg-info/requires.txt
uropa.egg-info/top_level.txt
utils/uropa2gtf.R
utils/uropa_reformat_output.R
utils/uropa_summary.R