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page_id: components page_type: components generation_mode: inferred freshness_status: updated updated_at: 2026-07-06T01:46:15.869Z

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    "component:examples/offscreen_webrtc_demo/signaling/package.json"
  ],
  "qualityWarnings": []
}

</details>

Components

Component inventory for Helix.

Component Inventory

  • Helix (application) at . with 882 files.
  • helix-governance (application) at . with 882 files.
  • src (module) at src with 881 files.
  • Tests (tests) at tests with 774 files.
  • Documentation (docs) at . with 242 files.
  • engine/src (module) at engine/src with 7 files.
  • github.com/omniscoder/Helix/tools/hubverifier-go (application) at tools/hubverifier-go with 6 files.
  • src/helix_engine/src (module) at src/helix_engine/src with 6 files.
  • offscreen-webrtc-signaling (application) at examples/offscreen_webrtc_demo/signaling with 2 files.
  • helix (application) at . with 1 files.
  • helix-campaign (application) at . with 1 files.
  • helix-cli (application) at . with 1 files.
<details> <summary>Related files:</summary>
  • requirements-dev.txt
  • src/helix_api.py
  • src/helix_cuda_fields.py
  • src/helix_engine/__init__.py
  • pyproject.toml
  • src/helix_engine/CMakeLists.txt
  • deliver_workbench/tests/__init__.py
  • deliver_workbench/tests/test_adapter_e2e.py
  • deliver_workbench/tests/test_database.py
  • deliver_workbench/tests/test_matchmaker.py
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
  • engine/src/helix/cuda/fields/composite_editability.cu
  • engine/src/helix/cuda/fields/dcas9_occupancy.cu
  • engine/src/helix/cuda/fields/gc_homopolymer.cu
  • engine/src/helix/cuda/fields/indel_risk.cu
  • tools/hubverifier-go/cmd/hubverify/main.go
  • tools/hubverifier-go/go.mod
  • tools/hubverifier-go/internal/c14n/c14n_test.go
  • tools/hubverifier-go/internal/c14n/c14n.go
  • src/helix_engine/src/binding.cpp
  • src/helix_engine/src/ctmc_tau_leap_cuda.cu
  • src/helix_engine/src/l0_thermo.cu
  • src/helix_engine/src/physics_cuda.cu
  • examples/offscreen_webrtc_demo/signaling/package.json
  • examples/offscreen_webrtc_demo/signaling/server.js
</details> <details> <summary>Citations:</summary>
  • requirements-dev.txt
  • src/helix_api.py
  • pyproject.toml
  • src/helix_cuda_fields.py
  • deliver_workbench/tests/__init__.py
  • deliver_workbench/tests/test_adapter_e2e.py:16
  • benchmarks/README.md
  • deliver_workbench/README.md
  • engine/src/helix/cuda/fields/composite_editability.cu
  • engine/src/helix/cuda/fields/dcas9_occupancy.cu
  • tools/hubverifier-go/cmd/hubverify/main.go:22
  • tools/hubverifier-go/go.mod
  • src/helix_engine/src/binding.cpp
  • src/helix_engine/src/ctmc_tau_leap_cuda.cu
  • examples/offscreen_webrtc_demo/signaling/package.json
  • examples/offscreen_webrtc_demo/signaling/server.js:6
</details>

Where to Look Next

Citations

<details> <summary>Citations:</summary>
  • requirements-dev.txt
  • src/helix_api.py
  • pyproject.toml
  • src/helix_cuda_fields.py
  • deliver_workbench/tests/__init__.py
  • deliver_workbench/tests/test_adapter_e2e.py:16
  • benchmarks/README.md
  • deliver_workbench/README.md
  • engine/src/helix/cuda/fields/composite_editability.cu
  • engine/src/helix/cuda/fields/dcas9_occupancy.cu
  • tools/hubverifier-go/cmd/hubverify/main.go:22
  • tools/hubverifier-go/go.mod
  • src/helix_engine/src/binding.cpp
  • src/helix_engine/src/ctmc_tau_leap_cuda.cu
  • examples/offscreen_webrtc_demo/signaling/package.json
  • examples/offscreen_webrtc_demo/signaling/server.js:6
</details>