LICENSE
README.md
pyproject.toml
setup.py
src/fp_tools/__init__.py
src/fp_tools/cli.py
src/fp_tools/cli_batch.py
src/fp_tools/cli_gui.py
src/fp_tools/cli_plotaggregate.py
src/fp_tools/cli_scorebigwig.py
src/fp_tools/gui_app.py
src/fp_tools/gui_config.py
src/fp_tools/gui_forms.py
src/fp_tools/gui_jobs.py
src/fp_tools/parsers.py
src/fp_tools/resources/__init__.py
src/fp_tools/resources/motifs/H14CORE_jaspar_format.txt
src/fp_tools/resources/motifs/H14INVITRO_jaspar_format.txt
src/fp_tools/resources/motifs/H14INVIVO_jaspar_format.txt
src/fp_tools/resources/motifs/H14RSNP_jaspar_format.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_fungi_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_insects_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_nematodes_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_plants_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_urochordates_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/JASPAR2026_CORE_vertebrates_non-redundant_pfms_jaspar.txt
src/fp_tools/resources/motifs/__init__.py
src/fp_tools/tools/__init__.py
src/fp_tools/tools/atacorrect.py
src/fp_tools/tools/atacorrect_functions.py
src/fp_tools/tools/candidates.py
src/fp_tools/tools/diff_footprint_helpers.py
src/fp_tools/tools/diff_footprint_replicate_report.py
src/fp_tools/tools/diff_footprint_skew_report.py
src/fp_tools/tools/diff_footprints.py
src/fp_tools/tools/find_signature_fp.py
src/fp_tools/tools/footprint_competition.py
src/fp_tools/tools/match_motifs.py
src/fp_tools/tools/motif_aggregate_grid.py
src/fp_tools/tools/motif_discovery.py
src/fp_tools/tools/normalize_bigwig.py
src/fp_tools/tools/plot_aggregate.py
src/fp_tools/tools/plot_aggregate_batch.py
src/fp_tools/tools/prepare_atac.py
src/fp_tools/tools/prepare_atac_legacy.py
src/fp_tools/tools/pseudobulk.py
src/fp_tools/tools/pseudobulk_footprints.py
src/fp_tools/tools/rerank.py
src/fp_tools/tools/review_multi_comparisons.py
src/fp_tools/tools/score_bigwig.py
src/fp_tools/tools/tfbs_features.py
src/fp_tools/tools/tfbs_model.py
src/fp_tools/tools/variants.py
src/fp_tools/utils/__init__.py
src/fp_tools/utils/logger.py
src/fp_tools/utils/motif_databases.py
src/fp_tools/utils/motifs.py
src/fp_tools/utils/multiscale.py
src/fp_tools/utils/ngs.pyx
src/fp_tools/utils/normalization.py
src/fp_tools/utils/plotting_style.py
src/fp_tools/utils/project_layout.py
src/fp_tools/utils/regions.py
src/fp_tools/utils/sequences.pyx
src/fp_tools/utils/signals.pyx
src/fp_tools/utils/utilities.py
src/fp_tools_bio.egg-info/PKG-INFO
src/fp_tools_bio.egg-info/SOURCES.txt
src/fp_tools_bio.egg-info/dependency_links.txt
src/fp_tools_bio.egg-info/entry_points.txt
src/fp_tools_bio.egg-info/requires.txt
src/fp_tools_bio.egg-info/top_level.txt
tests/test_atacorrect_batch.py
tests/test_benchmark_scripts.py
tests/test_call_footprints_candidates.py
tests/test_candidates.py
tests/test_cli_and_config_smoke.py
tests/test_cli_golden_regressions.py
tests/test_compare_atac_profiles.py
tests/test_compare_diff_footprints_normalization.py
tests/test_core_handling.py
tests/test_diff_footprint_replicate_report.py
tests/test_diff_footprints_interactive_html.py
tests/test_docs_contract.py
tests/test_fixture_regressions.py
tests/test_footprint_competition.py
tests/test_lcmv_collection.py
tests/test_motif_aggregate_grid.py
tests/test_motif_databases.py
tests/test_motif_discovery.py
tests/test_multiscale_scoring.py
tests/test_normalization.py
tests/test_normalize_bigwig.py
tests/test_paper_assets.py
tests/test_pbmc5k_pseudobulk_markers.py
tests/test_plot_aggregate_batch.py
tests/test_plotaggregate_normalization.py
tests/test_prepare_atac.py
tests/test_progress_logging.py
tests/test_project_layout_paths.py
tests/test_pseudobulk.py
tests/test_public_api_aliases.py
tests/test_release_metadata.py
tests/test_rerank.py
tests/test_review_multi_comparisons.py
tests/test_tfbs_features.py
tests/test_tfbs_model.py
tests/test_variants.py