LICENSE
README.md
pyproject.toml
src/helix_api.py
src/helix_cuda_fields.py
src/helix_workflows.py
src/helix/__init__.py
src/helix/amino_acids.py
src/helix/api.py
src/helix/bioinformatics.py
src/helix/cli.py
src/helix/clock.py
src/helix/codon.py
src/helix/config.py
src/helix/contract_info.py
src/helix/cyclospectrum.py
src/helix/engine_benchmark.py
src/helix/entropy.py
src/helix/export_verify.py
src/helix/fs.py
src/helix/helix_cuda_fields.py
src/helix/metrics_utils.py
src/helix/nussinov_algorithm.py
src/helix/protein.py
src/helix/provenance.py
src/helix/rng.py
src/helix/run_engine.py
src/helix/scientific_contract.py
src/helix/slices.py
src/helix/snapshot_bundle.py
src/helix/temp.py
src/helix/triage.py
src/helix/user_config.py
src/helix/workflows.py
src/helix/artifacts/__init__.py
src/helix/artifacts/build.py
src/helix/artifacts/bundle.py
src/helix/artifacts/verify.py
src/helix/calibration/__init__.py
src/helix/calibration/bundle.py
src/helix/core/__init__.py
src/helix/core/cache.py
src/helix/core/graph.py
src/helix/core/invariants.py
src/helix/core/offtarget_heat.py
src/helix/core/scc.py
src/helix/core/scheduler.py
src/helix/crispr/__init__.py
src/helix/crispr/coords.py
src/helix/crispr/ctmc_tau_leap.py
src/helix/crispr/ctmc_tau_leap_contract.py
src/helix/crispr/cut_spectrum.py
src/helix/crispr/dag_api.py
src/helix/crispr/guide.py
src/helix/crispr/guide_export.py
src/helix/crispr/guide_objectives.py
src/helix/crispr/interaction_proxy.py
src/helix/crispr/kmm.py
src/helix/crispr/model.py
src/helix/crispr/on_target.py
src/helix/crispr/pam.py
src/helix/crispr/physics.py
src/helix/crispr/physics_gpu.py
src/helix/crispr/rules.py
src/helix/crispr/score.py
src/helix/crispr/simulate.py
src/helix/crispr/simulator.py
src/helix/crispr/dynamic/__init__.py
src/helix/crispr/dynamic/config.py
src/helix/crispr/dynamic/fate.py
src/helix/crispr/dynamic/measurement.py
src/helix/crispr/dynamic/repair.py
src/helix/crispr/dynamic/simulator.py
src/helix/crispr/dynamic/state.py
src/helix/crispr/dynamic/utils.py
src/helix/crispr/on_target_engines/__init__.py
src/helix/crispr/on_target_engines/ontargetx.py
src/helix/crispr/on_target_engines/physics.py
src/helix/crispr/ontargetx/__init__.py
src/helix/crispr/ontargetx/encoding.py
src/helix/datasets/__init__.py
src/helix/datasets/demo/demo_crispr_config.json
src/helix/datasets/demo/demo_prime_config.json
src/helix/datasets/dna/human.txt
src/helix/datasets/dna/plasmid_demo.fna
src/helix/datasets/partner/01_crispr_knockout_spry.json
src/helix/datasets/partner/02_crispr_hdr_spcas9_ngg.json
src/helix/datasets/partner/03_prime_insertion.json
src/helix/datasets/protein/demo_protein.faa
src/helix/datasets/validation_packs/__init__.py
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/manifest.json
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected/alleles.tsv
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected/indel_hist.json
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected/summary.json
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected/top_alleles.tsv
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected_negative/alleles.tsv
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected_negative/indel_hist.json
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected_negative/summary.json
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/expected_negative/top_alleles.tsv
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/inputs/amplicon.fasta
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/inputs/reads_R1.fastq.gz
src/helix/datasets/validation_packs/ampseq_indel_profile_v1/inputs/reads_R2.fastq.gz
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src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md
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src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md
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src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/inputs/cut_model_case1_observed.json
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src/helix/datasets/validation_packs/crisprresso_import_v1/README.md
src/helix/datasets/validation_packs/crisprresso_import_v1/manifest.json
src/helix/datasets/validation_packs/crisprresso_import_v1/expected/alleles.tsv
src/helix/datasets/validation_packs/crisprresso_import_v1/expected/editing_summary.tsv
src/helix/datasets/validation_packs/crisprresso_import_v1/expected/metadata.json
src/helix/datasets/validation_packs/crisprresso_import_v1/expected_negative/alleles.tsv
src/helix/datasets/validation_packs/crisprresso_import_v1/expected_negative/editing_summary.tsv
src/helix/datasets/validation_packs/crisprresso_import_v1/expected_negative/metadata.json
src/helix/datasets/validation_packs/crisprresso_import_v1/inputs/CRISPResso_output/Alleles_frequency_table.txt
src/helix/datasets/validation_packs/crisprresso_import_v1/inputs/CRISPResso_output/CRISPResso_info.json
src/helix/datasets/validation_packs/crisprresso_import_v1/inputs/CRISPResso_output/CRISPResso_quantification_of_editing_frequency.txt
src/helix/datasets/validation_packs/repro_bundle_v1/README.md
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