LICENSE
README.md
pyproject.toml
src/stat_agent/__init__.py
src/stat_agent/_compat.py
src/stat_agent/config.py
src/stat_agent.egg-info/PKG-INFO
src/stat_agent.egg-info/SOURCES.txt
src/stat_agent.egg-info/dependency_links.txt
src/stat_agent.egg-info/entry_points.txt
src/stat_agent.egg-info/requires.txt
src/stat_agent.egg-info/top_level.txt
src/stat_agent/agent/__init__.py
src/stat_agent/agent/ablation.py
src/stat_agent/agent/agent.py
src/stat_agent/agent/graph.py
src/stat_agent/agent/llm_backend.py
src/stat_agent/agent/loop.py
src/stat_agent/agent/policy.py
src/stat_agent/agent/state.py
src/stat_agent/agent/nodes/__init__.py
src/stat_agent/agent/nodes/common.py
src/stat_agent/agent/nodes/execution.py
src/stat_agent/agent/nodes/finishing.py
src/stat_agent/agent/nodes/planning.py
src/stat_agent/agent/nodes/selection.py
src/stat_agent/cli/__init__.py
src/stat_agent/cli/chat.py
src/stat_agent/cli/main.py
src/stat_agent/cli/session_cmd.py
src/stat_agent/core/__init__.py
src/stat_agent/core/colors.py
src/stat_agent/core/data_slice.py
src/stat_agent/core/lock.py
src/stat_agent/core/roi_manager.py
src/stat_agent/core/session.py
src/stat_agent/core/view.py
src/stat_agent/events/__init__.py
src/stat_agent/events/catalogue.py
src/stat_agent/events/emit.py
src/stat_agent/events/encoding.py
src/stat_agent/extras/__init__.py
src/stat_agent/extras/deepagents_driver.py
src/stat_agent/extras/research.py
src/stat_agent/io/__init__.py
src/stat_agent/io/dataset.py
src/stat_agent/io/session_store.py
src/stat_agent/ledger/__init__.py
src/stat_agent/ledger/mutator.py
src/stat_agent/ledger/provenance.py
src/stat_agent/llm/__init__.py
src/stat_agent/llm/calllog.py
src/stat_agent/llm/client.py
src/stat_agent/llm/fake.py
src/stat_agent/llm/models.py
src/stat_agent/llm/structured.py
src/stat_agent/llm/usage.py
src/stat_agent/logging/__init__.py
src/stat_agent/logging/notebook.py
src/stat_agent/logging/report.py
src/stat_agent/memory/__init__.py
src/stat_agent/memory/context.py
src/stat_agent/memory/state.py
src/stat_agent/prompts/__init__.py
src/stat_agent/prompts/analyzer.v1.md
src/stat_agent/prompts/analyzer.v2.md
src/stat_agent/prompts/generator_system.v1.md
src/stat_agent/prompts/generator_system.v2.md
src/stat_agent/prompts/generator_user.v1.md
src/stat_agent/prompts/generator_user.v2.md
src/stat_agent/prompts/matcher.v1.md
src/stat_agent/prompts/matcher.v2.md
src/stat_agent/prompts/method_card.v1.md
src/stat_agent/prompts/planner.v1.md
src/stat_agent/prompts/planner.v2.md
src/stat_agent/prompts/reflector.v1.md
src/stat_agent/prompts/skill_author.v1.md
src/stat_agent/prompts/summarizer.v1.md
src/stat_agent/prompts/verifier.v1.md
src/stat_agent/roles/__init__.py
src/stat_agent/roles/analyzer.py
src/stat_agent/roles/base.py
src/stat_agent/roles/generator.py
src/stat_agent/roles/matcher.py
src/stat_agent/roles/method_card.py
src/stat_agent/roles/planner.py
src/stat_agent/roles/reflector.py
src/stat_agent/roles/summarizer.py
src/stat_agent/roles/verifier.py
src/stat_agent/runtime/__init__.py
src/stat_agent/runtime/artifacts.py
src/stat_agent/runtime/executor.py
src/stat_agent/runtime/plots.py
src/stat_agent/runtime/safety.py
src/stat_agent/runtime/snapshot.py
src/stat_agent/skills/__init__.py
src/stat_agent/skills/author.py
src/stat_agent/skills/cli.py
src/stat_agent/skills/filter.py
src/stat_agent/skills/lint.py
src/stat_agent/skills/loader.py
src/stat_agent/skills/registry.py
src/stat_agent/skills/schema.py
src/stat_agent/skills/alignment-STalign/SKILL.md
src/stat_agent/skills/alignment-STalign/STalign/STalign.py
src/stat_agent/skills/alignment-STalign/STalign/__init__.py
src/stat_agent/skills/alignment-STalign/STalign/curve_annotator.py
src/stat_agent/skills/alignment-STalign/STalign/point_annotator.py
src/stat_agent/skills/annotation-tangram/SKILL.md
src/stat_agent/skills/cell-communication-CellPhoneDB/SKILL.md
src/stat_agent/skills/cell-communication-LIANA/SKILL.md
src/stat_agent/skills/celltype-annotation-GPT/SKILL.md
src/stat_agent/skills/celltype-annotation-GPT/celltype_fast/__init__.py
src/stat_agent/skills/celltype-annotation-GPT/celltype_fast/annotation_clustering.py
src/stat_agent/skills/celltype-annotation-scANVI/SKILL.md
src/stat_agent/skills/celltype-annotation-scANVI/celltype_scvi/__init__.py
src/stat_agent/skills/celltype-annotation-scANVI/celltype_scvi/annotation_scvi.py
src/stat_agent/skills/celltype-deconvolution-RCTD/SKILL.md
src/stat_agent/skills/celltype-deconvolution-RCTD/deconv_rctd/RCTD.py
src/stat_agent/skills/celltype-deconvolution-RCTD/deconv_rctd/__init__.py
src/stat_agent/skills/celltype-deconvolution-RCTD/deconv_rctd/data_utils.py
src/stat_agent/skills/deconvolution-cell2location/SKILL.md
src/stat_agent/skills/deconvolution-flashdeconv/SKILL.md
src/stat_agent/skills/differential-expression/SKILL.md
src/stat_agent/skills/enrichment-ora-ssgsea/SKILL.md
src/stat_agent/skills/integration-Harmony/SKILL.md
src/stat_agent/skills/integration-bbknn/SKILL.md
src/stat_agent/skills/integration-scanorama/SKILL.md
src/stat_agent/skills/niche-detection-Harmonics/SKILL.md
src/stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/__init__.py
src/stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/hypo_test.py
src/stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/model.py
src/stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/utils.py
src/stat_agent/skills/pathway-GO-enrichment/SKILL.md
src/stat_agent/skills/pathway-enrichment-compare/SKILL.md
src/stat_agent/skills/pathway-ssgsea/SKILL.md
src/stat_agent/skills/registration-paste/SKILL.md
src/stat_agent/skills/spatial-domain-GraphST/SKILL.md
src/stat_agent/skills/spatial-domain-STAGATE/SKILL.md
src/stat_agent/skills/spatial-domain-SpaGCN/SKILL.md
src/stat_agent/skills/spatial-statistics-squidpy/SKILL.md
src/stat_agent/skills/spatial-stats-neighborhood-enrichment/SKILL.md
src/stat_agent/skills/svg-SpatialDE/SKILL.md
src/stat_agent/skills/trajectory-palantir-dpt/SKILL.md
src/stat_agent/web/__init__.py
src/stat_agent/web/__main__.py
src/stat_agent/web/errors.py
src/stat_agent/web/events.py
src/stat_agent/web/render.py
src/stat_agent/web/schemas.py
src/stat_agent/web/server.py
src/stat_agent/web/state.py
src/stat_agent/web/turns.py
src/stat_agent/web/routes/__init__.py
src/stat_agent/web/routes/common.py
src/stat_agent/web/routes/data.py
src/stat_agent/web/routes/misc.py
src/stat_agent/web/routes/rois.py
src/stat_agent/web/routes/session.py
src/stat_agent/web/routes/turns.py
src/stat_agent/web/static/css/style.css
src/stat_agent/web/static/js/app.js
src/stat_agent/web/templates/index.html
src/stat_bench/__init__.py
src/stat_bench/cli.py
src/stat_bench/corrupt.py
src/stat_bench/judge.py
src/stat_bench/replay.py
src/stat_bench/result.py
src/stat_bench/runner.py
src/stat_bench/suite.py
src/stat_bench/summarize.py
src/stat_bench/score/__init__.py
src/stat_bench/score/sse.py
src/stat_bench/session_bench/__init__.py
src/stat_bench/session_bench/runner.py
src/stat_bench/session_bench/verifiers.py
src/stat_bench/suites/sessionbench/CO-1_correction.yaml
src/stat_bench/suites/sessionbench/CR-1_cross_turn_reference.yaml
src/stat_bench/suites/sessionbench/OR-1_out_of_registry.yaml
src/stat_bench/suites/sessionbench/RE-1_recovery.yaml
src/stat_bench/systems/__init__.py
src/stat_bench/systems/base.py
src/stat_bench/systems/stat.py
src/stat_bench/trace/__init__.py
src/stat_bench/trace/parse.py