Application Features Reference
This chapter is a structured reference of major Coyote3 features and where they live in the app.
Use it as a “what can I do?” map.
Related:
1. Worklist and Case Access
Main routes:
/samples/samples/live/samples/done
Capabilities:
- find samples by search
- switch live/done views
- open DNA and RNA workspaces
- jump to sample settings
- open saved reports
2. Sample Settings and Gene Scope Control
Main route:
/samples/<sample_id>/edit
Capabilities:
- apply/remove ISGL lists
- add/clear ad hoc genes
- inspect effective genes
- inspect raw vs filtered variant stats
3. DNA Analysis Features
Main route:
Capabilities:
- section-based variant review (SNV/CNV/translocation/biomarker depending on assay config)
- variant detail pages
- manual classification and comment actions
- report preview and save
- history links to reported occurrence context
4. RNA Analysis Features
Main route:
/rna/sample/<sample_id>K=
Capabilities:
- fusion candidate review
- false-positive handling
- sample comments
- report preview and PDF export
5. Reporting and Historical Retrieval
Main routes:
/samples/<sample_id>/reports/<report_id>/samples/<sample_id>/reports/<report_id>/download/reported_variants/variant/<variant_id>/<tier>
Capabilities:
- open/download saved report artifacts
- review report-linked historical variant snapshots
6. Navbar Discovery Features
Main routes:
MATRIX: /assay-catalog-matrixCATALOG: /assay-catalogVARIANT SEARCH: /search/tiered_variants
Capabilities:
- matrix-based gene coverage discovery
- modality/category/list drill-down and CSV export
- cross-sample annotation/report search with mode/filter controls
Full guide:
7. Admin Governance Features (for authorized users)
Main routes:
/admin/users/admin/roles/admin/permissions/admin/schemas/admin/asp/manage/admin/aspc/admin/genelists/admin/audit
Capabilities:
- user/role/access governance
- schema-driven config management
- assay panel and assay runtime configuration
- In Silico Gene List (ISGL) management
- audit review
Full guide:
8. Docs and In-App Knowledge Features
Main routes:
- docs home:
/handbook/
- user handbook:
/handbook/user
Capabilities:
- keyword search across handbook pages
- grouped handbook links by track
- cross-linked chapter navigation