LICENSE
MANIFEST.in
README.rst
make_docs.py
pyproject.toml
run-test.py
setup.cfg
test.h5
bin/lisa
cistrome_processing/Snakefile
cistrome_processing/config.yaml
cistrome_processing/.ipynb_checkpoints/Untitled-checkpoint.ipynb
cistrome_processing/bin/append_peak_indices.py
cistrome_processing/bin/append_profiles.py
cistrome_processing/bin/calc_motif_bins.py
cistrome_processing/bin/compute_coverage_array.py
cistrome_processing/bin/map_peaks_to_indices.py
cistrome_processing/motif_pipeline/Motif_mm10_50.done
cistrome_processing/motif_pipeline/Snakefile
cistrome_processing/motif_pipeline/config.yaml
cistrome_processing/motif_pipeline/motifs.txt
cistrome_processing/motif_pipeline/bin/add_motifs_to_h5.py
cistrome_processing/motif_pipeline/bin/get_motif_bins.py
cistrome_processing/old_pipeline/Snakefile
cistrome_processing/old_pipeline/config.yaml
cistrome_processing/old_pipeline/bin/append_peak_indices.py
cistrome_processing/old_pipeline/bin/append_profiles.py
cistrome_processing/old_pipeline/bin/calc_motif_bins.py
cistrome_processing/old_pipeline/bin/compute_coverage_array.py
cistrome_processing/old_pipeline/bin/map_peaks_to_indices.py
data_conversion/hg38_lisa1_data_conversion.ipynb
data_conversion/lisa1_data.ini
data_conversion/mm10_lisa1_data_conversion.ipynb
docs/.DS_Store
docs/.Rhistory
docs/DataAnalysisGuide.md
docs/cli.rst
docs/cluster_profile.png
docs/example_clustermap.png
docs/fromGenes.png
docs/fromRegions.png
docs/lisa_web_ui.png
docs/model_diagram.png
docs/output_24_1.png
docs/output_31_0.png
docs/output_34_0.png
docs/output_36_0.png
docs/output_40_0.png
docs/output_56_1.png
docs/output_79_0.png
docs/output_7_1.png
docs/output_82_1.png
docs/python_api.rst
docs/troubleshooting.md
docs/user_guide.md
evaluation/eval_lisa_rank.py
lisa/__init__.py
lisa/_version.py
lisa/.ipynb_checkpoints/Untitled-checkpoint.ipynb
lisa/__pycache__/__init__.cpython-36.pyc
lisa/__pycache__/__init__.cpython-37.pyc
lisa/__pycache__/__init__.cpython-38.pyc
lisa/__pycache__/_version.cpython-38.pyc
lisa/__pycache__/assays.cpython-38.pyc
lisa/__pycache__/gene_selection.cpython-38.pyc
lisa/__pycache__/lisa.cpython-36.pyc
lisa/__pycache__/lisa.cpython-37.pyc
lisa/__pycache__/lisa.cpython-38.pyc
lisa/__pycache__/models.cpython-38.pyc
lisa/__pycache__/utils.cpython-38.pyc
lisa/cli/__init__.py
lisa/cli/cli.py
lisa/cli/test_cli.py
lisa/core/__init__.py
lisa/core/assays.py
lisa/core/config.ini
lisa/core/data_interface.py
lisa/core/gene_selection.py
lisa/core/genome_tools.py
lisa/core/h5_config.ini
lisa/core/io.py
lisa/core/lisa_core.py
lisa/core/utils.py
lisa/genomes/hg38.genome
lisa/genomes/hg38.refseq
lisa/genomes/mm10.genome
lisa/genomes/mm10.refseq
lisa/lisa_public_data/__init__.py
lisa/lisa_public_data/assays.py
lisa/lisa_public_data/config.ini
lisa/lisa_public_data/genes_test.py
lisa/lisa_public_data/models.py
lisa/lisa_user_data/__init__.py
lisa/lisa_user_data/assays.py
lisa/lisa_user_data/bam_test.py
lisa/lisa_user_data/config.ini
lisa/lisa_user_data/coverage_test.py
lisa/lisa_user_data/regions_test.py
lisa2.egg-info/PKG-INFO
lisa2.egg-info/SOURCES.txt
lisa2.egg-info/dependency_links.txt
lisa2.egg-info/entry_points.txt
lisa2.egg-info/requires.txt
lisa2.egg-info/top_level.txt
lisa2.egg-info/zip-safe
tests/test_data_interface.py
tests/test_genome_tools.py