LICENSE
README.md
pyproject.toml
stat_agent/__init__.py
stat_agent/_compat.py
stat_agent.egg-info/PKG-INFO
stat_agent.egg-info/SOURCES.txt
stat_agent.egg-info/dependency_links.txt
stat_agent.egg-info/entry_points.txt
stat_agent.egg-info/requires.txt
stat_agent.egg-info/top_level.txt
stat_agent/agent/__init__.py
stat_agent/agent/clarification_context.py
stat_agent/agent/conversation_orchestrator.py
stat_agent/agent/error_reflection.py
stat_agent/agent/executor.py
stat_agent/agent/llm_backend.py
stat_agent/agent/memory.py
stat_agent/agent/model_config.py
stat_agent/agent/notebook_logger.py
stat_agent/agent/pipeline_executor.py
stat_agent/agent/prompt_logger.py
stat_agent/agent/query_planner.py
stat_agent/agent/skill_filter.py
stat_agent/agent/skill_registry.py
stat_agent/agent/skill_verifier.py
stat_agent/agent/spatial_agent_core.py
stat_agent/agent/tools.py
stat_agent/core/__init__.py
stat_agent/core/data_slice.py
stat_agent/core/roi_manager.py
stat_agent/core/session.py
stat_agent/functions/__init__.py
stat_agent/functions/io.py
stat_agent/skills/__init__.py
stat_agent/skills/alignment-STalign/SKILL.md
stat_agent/skills/alignment-STalign/STalign/STalign.py
stat_agent/skills/alignment-STalign/STalign/__init__.py
stat_agent/skills/alignment-STalign/STalign/curve_annotator.py
stat_agent/skills/alignment-STalign/STalign/point_annotator.py
stat_agent/skills/annotation-tangram/SKILL.md
stat_agent/skills/cell-communication-CellPhoneDB/SKILL.md
stat_agent/skills/cell-communication-LIANA/SKILL.md
stat_agent/skills/celltype-annotation-GPT/SKILL.md
stat_agent/skills/celltype-annotation-GPT/celltype_fast/__init__.py
stat_agent/skills/celltype-annotation-GPT/celltype_fast/annotation_clustering.py
stat_agent/skills/celltype-annotation-scANVI/SKILL.md
stat_agent/skills/celltype-annotation-scANVI/celltype_scvi/__init__.py
stat_agent/skills/celltype-annotation-scANVI/celltype_scvi/annotation_scvi.py
stat_agent/skills/celltype-deconvolution-RCTD/SKILL.md
stat_agent/skills/celltype-deconvolution-RCTD/deconv_rctd/RCTD.py
stat_agent/skills/celltype-deconvolution-RCTD/deconv_rctd/__init__.py
stat_agent/skills/celltype-deconvolution-RCTD/deconv_rctd/data_utils.py
stat_agent/skills/cnv-infercnvpy/SKILL.md
stat_agent/skills/deconvolution-cell2location/SKILL.md
stat_agent/skills/deconvolution-flashdeconv/SKILL.md
stat_agent/skills/differential-expression/SKILL.md
stat_agent/skills/enrichment-ora-ssgsea/SKILL.md
stat_agent/skills/integration-Harmony/SKILL.md
stat_agent/skills/integration-bbknn/SKILL.md
stat_agent/skills/integration-scanorama/SKILL.md
stat_agent/skills/niche-detection-Harmonics/SKILL.md
stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/__init__.py
stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/hypo_test.py
stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/model.py
stat_agent/skills/niche-detection-Harmonics/niche_analysis_lib/utils.py
stat_agent/skills/pathway-GO-enrichment/SKILL.md
stat_agent/skills/pathway-enrichment-compare/SKILL.md
stat_agent/skills/pathway-ssgsea/SKILL.md
stat_agent/skills/registration-paste/SKILL.md
stat_agent/skills/spatial-domain-GraphST/SKILL.md
stat_agent/skills/spatial-domain-STAGATE/SKILL.md
stat_agent/skills/spatial-domain-SpaGCN/SKILL.md
stat_agent/skills/spatial-statistics-squidpy/SKILL.md
stat_agent/skills/spatial-stats-neighborhood-enrichment/SKILL.md
stat_agent/skills/svg-SpatialDE/SKILL.md
stat_agent/skills/trajectory-palantir-dpt/SKILL.md
stat_agent/web/__init__.py
stat_agent/web/app.py
stat_agent/web/static/css/style.css
stat_agent/web/static/js/app.js
stat_agent/web/templates/index.html
tests/test_celltype_optional.py
tests/test_llm_skill_matching.py
tests/test_new_pipeline.py
tests/test_niche_detection_integration.py