LICENSE
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.py
tests/test_agent_presets.py
tests/test_compact_report.py
tests/test_custom.py
tests/test_empty_probe_results.py
tests/test_excel_results.py
tests/test_expression.py
tests/test_generated_defaults.py
tests/test_genome_fetch.py
tests/test_genome_router.py
tests/test_gtf_gene_names.py
tests/test_http_persistence.py
tests/test_hybridization.py
tests/test_jellyfish_index.py
tests/test_layout.py
tests/test_mrna_source.py
tests/test_offtarget_copies.py
tests/test_offtarget_expression.py
tests/test_offtarget_pool.py
tests/test_offtarget_search.py
tests/test_post_process_regions.py
tests/test_probe.py
tests/test_probe_index.py
tests/test_regions.py
tests/test_result_archive.py
tests/test_run_summary.py
tests/test_sampling.py
tests/test_sequence_filters.py
tests/test_skill.py
tests/test_task_control.py
tests/test_temperature_compatibility.py
tests/test_templates.py
tests/test_threads.py
tests/test_transcript_expression.py
tests/test_transcript_extraction.py
tests/test_transcript_index.py
tests/test_validate.py
tests/test_web_agent_optional.py
tests/test_workflow.py
uprobe/__init__.py
uprobe/__main__.py
uprobe.egg-info/PKG-INFO
uprobe.egg-info/SOURCES.txt
uprobe.egg-info/dependency_links.txt
uprobe.egg-info/entry_points.txt
uprobe.egg-info/not-zip-safe
uprobe.egg-info/requires.txt
uprobe.egg-info/top_level.txt
uprobe/core/.readthedocs.yaml
uprobe/core/__init__.py
uprobe/core/api.py
uprobe/core/cli.py
uprobe/core/copies.py
uprobe/core/gene_expression.py
uprobe/core/genome_fetch.py
uprobe/core/hybridization.py
uprobe/core/layout.py
uprobe/core/offtarget.py
uprobe/core/sampling.py
uprobe/core/utils.py
uprobe/core/validate.py
uprobe/core/attributes/__init__.py
uprobe/core/attributes/_attributes.py
uprobe/core/gen/__init__.py
uprobe/core/gen/barcodes.py
uprobe/core/gen/expression.py
uprobe/core/gen/fun.py
uprobe/core/gen/probe.py
uprobe/core/gen/utils.py
uprobe/core/process/__init__.py
uprobe/core/process/equal_space.py
uprobe/core/process/off_target_pool.py
uprobe/core/process/otp.py
uprobe/core/process/regions.py
uprobe/core/process/sequence_filter.py
uprobe/core/process/summary.py
uprobe/core/report/__init__.py
uprobe/core/report/compact.py
uprobe/core/report/excel.py
uprobe/core/report/formatting.py
uprobe/core/report/html.py
uprobe/core/report/plot.py
uprobe/core/report/run_summary.py
uprobe/core/tools/__init__.py
uprobe/core/tools/aligner.py
uprobe/core/tools/kmerFilter.py
uprobe/http/__init__.py
uprobe/http/__main__.py
uprobe/http/server.py
uprobe/http/agent/__init__.py
uprobe/http/agent/output_sandbox.py
uprobe/http/agent/session_manager.py
uprobe/http/agent/templates/DEFAULT_PROTOCOL.yaml
uprobe/http/agent/templates/uprobe_team.md
uprobe/http/routers/__init__.py
uprobe/http/routers/agent.py
uprobe/http/routers/auth.py
uprobe/http/routers/custom_probes.py
uprobe/http/routers/genome.py
uprobe/http/routers/task.py
uprobe/http/routers/user.py
uprobe/http/routers/workflow.py
uprobe/http/utils/__init__.py
uprobe/http/utils/agent_store.py
uprobe/http/utils/file.py
uprobe/http/utils/logger.py
uprobe/http/utils/paths.py
uprobe/http/utils/probe.py
uprobe/http/utils/process_pool.py
uprobe/http/utils/result_archive.py
uprobe/http/utils/task_control.py
uprobe/http/utils/task_queue.py
uprobe/http/utils/uprobe_runner.py
uprobe/http/utils/utils.py
uprobe/skills/__init__.py
uprobe/skills/u-probe/SKILL.md
uprobe/skills/u-probe/references/concepts/hybridization-and-tm.md
uprobe/skills/u-probe/references/concepts/probe-architecture.md
uprobe/skills/u-probe/references/concepts/specificity.md
uprobe/skills/u-probe/references/concepts/targets-and-isoforms.md
uprobe/skills/u-probe/references/techniques/README.md
uprobe/skills/u-probe/references/techniques/double-hyb-rca.md
uprobe/skills/u-probe/references/techniques/exseq.md
uprobe/skills/u-probe/references/techniques/hcr-v3.md
uprobe/skills/u-probe/references/techniques/merfish.md
uprobe/skills/u-probe/references/techniques/mip-seq.md
uprobe/skills/u-probe/references/techniques/oligopaint-dna-fish.md
uprobe/skills/u-probe/references/techniques/openfish.md
uprobe/skills/u-probe/references/techniques/padlock-iss-hybiss.md
uprobe/skills/u-probe/references/techniques/prism.md
uprobe/skills/u-probe/references/techniques/raefish.md
uprobe/skills/u-probe/references/techniques/seqfish-plus.md
uprobe/skills/u-probe/references/techniques/smfish.md
uprobe/skills/u-probe/references/techniques/smifish.md
uprobe/skills/u-probe/references/techniques/starmap.md
uprobe/skills/u-probe/references/techniques/tddn-fish.md
uprobe/skills/u-probe/references/uprobe/template-qa.md
uprobe/skills/u-probe/references/uprobe/troubleshooting.md
uprobe/skills/u-probe/references/uprobe/workflow.md
uprobe/skills/u-probe/references/uprobe/yaml-reference.md
uprobe/skills/u-probe/scripts/check_probes.py
uprobe/templates/__init__.py
uprobe/templates/double_hyb_rca.yaml
uprobe/templates/hcr_v3.yaml
uprobe/templates/merfish.yaml
uprobe/templates/mipseq.yaml
uprobe/templates/oligopaint.yaml
uprobe/templates/padlock_iss.yaml
uprobe/templates/seqfish_plus.yaml
uprobe/templates/smfish_stellaris.yaml
uprobe/templates/starmap.yaml