.gitignore
LICENSE
README.md
pyproject.toml
.github/workflows/release.yml
docs/01_data_prep.md
docs/02_snv.md
docs/03_scan.md
docs/04_motifs.md
docs/05_python_api.md
docs/06_masks_and_calibration.md
docs/07_yaml.md
docs/aff_rand_synthetic.png
docs/eubar_summary.png
docs/tert_promoter-best_pval.png
docs/tert_promoter.png
docs/GABPA/GABPA.logo_bits.png
docs/GABPA/GABPA.logo_bits_rc.png
docs/GABPA/GABPA.logo_prob.png
docs/GABPA/GABPA.logo_prob_rc.png
docs/GABPA/GABPA.meme
docs/GABPA/GABPA.ppm.tsv
docs/GABPA/GABPA.reduced.tsv
docs/GABPA/GABPA.reduced_enrichment.png
docs/GABPA/GABPA.reduced_enrichment_rc.png
docs/GABPA/GABPA.reduced_full.tsv
docs/GABPA/GABPA.seed_enrichment_curve.png
docs/GABPA/GABPA.seed_escore_hist.png
docs/GABPA/GABPA.seed_roc.png
docs/GABPA/GABPA.top_escores.tsv
eubar/__init__.py
eubar/__main__.py
eubar/api.py
eubar/array.py
eubar/calibrate.py
eubar/cli.py
eubar/cli_options.py
eubar/config.py
eubar/intensities.py
eubar/motifs.py
eubar/pytest.ini
eubar/run.py
eubar/scan.py
eubar/snv.py
eubar/task_config.py
eubar/template.py
eubar.egg-info/PKG-INFO
eubar.egg-info/SOURCES.txt
eubar.egg-info/dependency_links.txt
eubar.egg-info/entry_points.txt
eubar.egg-info/requires.txt
eubar.egg-info/scm_file_list.json
eubar.egg-info/scm_version.json
eubar.egg-info/top_level.txt
eubar/core/__init__.py
eubar/core/analyze.py
eubar/core/calibration.py
eubar/core/calibration_reporting.py
eubar/core/data.py
eubar/core/design.py
eubar/core/inspect.py
eubar/core/masking.py
eubar/core/matching.py
eubar/core/motif_data.py
eubar/core/motif_mask.py
eubar/core/motif_output.py
eubar/core/motif_search.py
eubar/core/patterns.py
eubar/core/pooled.py
eubar/core/rand.py
eubar/core/regression.py
eubar/core/reporting.py
eubar/core/sampling.py
eubar/core/sequence.py
eubar/core/snv_results.py
eubar/templates/array.yaml
eubar/templates/calibrate_mask.yaml
eubar/templates/calibrate_max_probes.yaml
eubar/templates/intensities.yaml
eubar/templates/motifs.yaml
eubar/templates/pipeline.yaml
eubar/templates/scan.yaml
eubar/templates/snv.yaml
eubar/tests/README.md
eubar/tests/conftest.py
eubar/tests/execution_cases.py
eubar/tests/output_comparison.py
eubar/tests/test_calibrate_public_cli.py
eubar/tests/test_calibration_reports.py
eubar/tests/test_calibration_rules.py
eubar/tests/test_cli_contract.py
eubar/tests/test_execution.py
eubar/tests/test_masks.py
eubar/tests/test_matching_regression.py
eubar/tests/test_motifs_contract.py
eubar/tests/test_output_comparison.py
eubar/tests/test_patterns_extra.py
eubar/tests/test_rand_determinism.py
eubar/tests/test_result_edges.py
eubar/tests/test_snv_statistics.py
eubar/tests/test_task_api.py
eubar/tests/test_yaml_config.py
eubar/tests/fixtures/README.md
eubar/tests/fixtures/array.tsv
eubar/tests/fixtures/genome.fa
eubar/tests/fixtures/genome.fa.fai
eubar/tests/fixtures/intensities.tsv
eubar/tests/fixtures/probes.bed
eubar/tests/fixtures/reference-environment.txt
eubar/tests/fixtures/signal.bw
eubar/tests/fixtures/variants.txt
eubar/tests/fixtures/expected/intensities.tsv
eubar/tests/fixtures/expected/mask_calibration/cal.families.tsv
eubar/tests/fixtures/expected/mask_calibration/cal.family_curves.tsv
eubar/tests/fixtures/expected/mask_calibration/cal.recommendation.tsv
eubar/tests/fixtures/expected/mask_calibration/cal.summary.tsv
eubar/tests/fixtures/expected/max_probes/cal.contrasts.tsv
eubar/tests/fixtures/expected/max_probes/cal.family_curves.tsv
eubar/tests/fixtures/expected/max_probes/cal.pvalue_quartiles.tsv
eubar/tests/fixtures/expected/max_probes/cal.recommendation.tsv
eubar/tests/fixtures/expected/max_probes/cal.summary.tsv
eubar/tests/fixtures/expected/motifs/motif.meme
eubar/tests/fixtures/expected/motifs/motif.ppm.tsv
eubar/tests/fixtures/expected/motifs/motif.reduced.tsv
eubar/tests/fixtures/expected/motifs/motif.reduced_full.tsv
eubar/tests/fixtures/expected/motifs/motif.top_escores.tsv
eubar/tests/fixtures/expected/motifs_extend/motif.meme
eubar/tests/fixtures/expected/motifs_extend/motif.ppm.tsv
eubar/tests/fixtures/expected/motifs_extend/motif.reduced.tsv
eubar/tests/fixtures/expected/motifs_extend/motif.reduced_full.tsv
eubar/tests/fixtures/expected/motifs_extend/motif.top_escores.tsv
eubar/tests/fixtures/expected/motifs_mask/motif.meme
eubar/tests/fixtures/expected/motifs_mask/motif.ppm.tsv
eubar/tests/fixtures/expected/motifs_mask/motif.reduced.tsv
eubar/tests/fixtures/expected/motifs_mask/motif.reduced_full.tsv
eubar/tests/fixtures/expected/motifs_mask/motif.top_escores.tsv
eubar/tests/fixtures/expected/scan/stdout.txt
eubar/tests/fixtures/expected/scan_holm/stdout.txt
eubar/tests/fixtures/expected/scan_holm_reverse/stdout.txt
eubar/tests/fixtures/expected/scan_pooled/stdout.txt
eubar/tests/fixtures/expected/snv/stdout.txt
eubar/tests/fixtures/expected/snv_best/stdout.txt
eubar/tests/fixtures/expected/snv_best_holm_cap/stdout.txt
eubar/tests/fixtures/expected/snv_mask/stdout.txt
eubar/tests/fixtures/expected/snv_mask_asymmetric_best_holm_cap/stdout.txt
eubar/tests/fixtures/expected/snv_mask_best_holm_cap/stdout.txt
eubar/tests/fixtures/help/array.txt
eubar/tests/fixtures/help/calibrate.txt
eubar/tests/fixtures/help/intensities.txt
eubar/tests/fixtures/help/motifs.txt
eubar/tests/fixtures/help/run.txt
eubar/tests/fixtures/help/scan.txt
eubar/tests/fixtures/help/snv.txt
eubar/tests/fixtures/help/template.txt