.dockerignore
Dockerfile
LICENSE
README.md
pyproject.toml
requirements.txt
run_sponge.py
.github/workflows/publish_package.yaml
.github/workflows/publish_pypi.yaml
.github/workflows/publish_testpypi.yaml
.github/workflows/test.yaml
.github/workflows/test_testpypi_install.yaml
netzoopy_sponge.egg-info/PKG-INFO
netzoopy_sponge.egg-info/SOURCES.txt
netzoopy_sponge.egg-info/dependency_links.txt
netzoopy_sponge.egg-info/entry_points.txt
netzoopy_sponge.egg-info/requires.txt
netzoopy_sponge.egg-info/top_level.txt
sponge/__init__.py
sponge/cli.py
sponge/config.yaml
sponge/config_manager.py
sponge/sponge.py
sponge/user_config.yaml
sponge/modules/__init__.py
sponge/modules/analysis/__init__.py
sponge/modules/analysis/analysis.py
sponge/modules/data_retriever/__init__.py
sponge/modules/data_retriever/data_retriever.py
sponge/modules/data_retriever/file_retriever.py
sponge/modules/data_retriever/region_retriever.py
sponge/modules/data_retriever/tfbs_retriever.py
sponge/modules/file_writer/__init__.py
sponge/modules/file_writer/file_writer.py
sponge/modules/match_aggregator/__init__.py
sponge/modules/match_aggregator/match_aggregator.py
sponge/modules/match_filter/__init__.py
sponge/modules/match_filter/match_filter.py
sponge/modules/motif_selector/__init__.py
sponge/modules/motif_selector/homology_retriever.py
sponge/modules/motif_selector/jaspar_retriever.py
sponge/modules/motif_selector/motif_selector.py
sponge/modules/ppi_retriever/__init__.py
sponge/modules/ppi_retriever/ppi_retriever.py
sponge/modules/protein_id_mapper/__init__.py
sponge/modules/protein_id_mapper/protein_id_mapper.py
sponge/modules/utils/__init__.py
sponge/modules/utils/data_retrieval.py
sponge/modules/utils/dictionary_update.py
sponge/modules/utils/jaspar_versioning.py
sponge/modules/utils/motif_information.py
sponge/modules/utils/string_manipulation.py
sponge/modules/utils/tfbs_filtering.py
sponge/modules/version_logger/__init__.py
sponge/modules/version_logger/version_logger.py
tests/test_sponge.py
tests/sponge/JASPAR.bb
tests/sponge/chr19_subset.bb
tests/sponge/chr19_subset.tsv
tests/sponge/comp_motif_prior_1.tsv
tests/sponge/comp_motif_prior_2.tsv
tests/sponge/foxf2_chr19_subset.tsv
tests/sponge/test_motif_prior.tsv
tests/sponge/test_ppi_prior.tsv
tests/sponge/test_user_config.yaml