Triage experimental screen hits from supplied guide counts

Why use this

1. A researcher reviewing an experimental screen may need to aggregate guide-level observations without losing sample labels, annotation provenance or the distinction between exploratory ranking and biological confirmation. A polished ranking can hide input mismatches or incomplete annotations.

2. This job could prepare a transparent triage-analysis specification and evidence checklist. Keeping aggregation choices and missing data visible helps qualified researchers decide which later results deserve follow-up, without expanding into experimental design or clinical interpretation.

Why an agent / simpler alternative

Useful judgment

Reconcile supplied count/annotation manifests, identify aggregation ambiguities and organize traceability for expert review.

Simpler alternative

Use an established analysis pipeline when the assay and data structure match its documented assumptions.

Unsuitable when

The workflow would design guides, fetch unapproved annotations or claim therapeutic/clinical actionability.

Proposed inputs

1. Name

   Guide-count manifest

   Owner

   Authorized researcher

   Minimum scope

   Supplied identifiers, sample labels and count provenance

   Quality check

   Check duplicate guides, missing values and group alignment

2. Name

   Approved analysis/annotations

   Owner

   Domain lead

   Minimum scope

   Provided gene mappings, metadata and aggregation choices

   Quality check

   Record annotation versions and unresolved mappings

Access and setup — proposed or unknown

Proposed minimum

1. Review synthetic placeholder counts and metadata schemas; no analysis execution, biological design or external annotation retrieval.

Compatibility unknowns

1. Current data support, aggregation implementation, scientific adequacy and runtime compatibility are unknown.

External actions requiring approval

1. Sensitive-data access, computation, output overwrites and sharing research results requires approved scope.

Expected deliverable and review checks

Proposed artifact

Triage-plan candidate with input exceptions, aggregation traceability and expert-review requirements for any future ranking.

Critical checks

1. Preserve guide-to-gene mappings; distinguish missing counts from zero; retain annotations by provenance; do not equate rank with validated effect.

Missing output evidence

This overlay adds no new output inspection, execution or validation; consult the referenced canonical source outcome limits.

Failure signals and proposed responses

1. Signal

   One guide maps ambiguously to a gene

   Why it matters

   Aggregation may attribute evidence incorrectly

   Proposed response

   Hold the mapping for researcher resolution.

2. Signal

   Sample labels are reversed

   Why it matters

   The intended comparison changes meaning

   Proposed response

   Verify labels against the supplied design before any calculation.

Effort and cost — unknown

Setup work

1. Define input contracts and permitted analysis boundaries.

Ongoing review

1. Researchers review actual analysis evidence and decide on follow-up independently.

Unknowns

1. Assay quality, mapping validity, statistical suitability and analysis costs are unknown.

First check — proposed, unexecuted

Status

proposed_unexecuted

Synthetic fixture

Invent placeholder guides G-A/G-B with an ambiguous mapping and swapped sample labels; prepare a preflight report only.

Acceptance checks

1. Flag both issues; rank no real targets; design no experiment and claim no biological validation.

Stop conditions

1. Stop if provenance, mapping or scientific authority is unresolved.

Limits

1. A triage plan cannot establish experimental hits, biological mechanisms or clinical relevance.