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Plugin / OpenAI

Life Sciences NGS Analysis Codex Plugin

Guided NGS routing and local execution for sequencing analysis.

Docs reviewedChecked 2026-09-20Runtime not tested

What it adds

A guided intake, routing, and execution plugin for next-generation sequencing workflows. It helps Codex inspect local sequencing inputs, ask only the missing assay-specific questions, choose public or freely accessible runtime-installable packages where possible, check existing tool availability before any install, and execute supported local workflows with validation, logs, manifests, QC reports, and artifact indexes. It includes deeper decision skills for BCL demultiplexing, FASTQ QC execution and interpretation, germline, somatic and UMI-panel DNA variants, bulk RNA-seq count generation and differential expression, ATAC-seq, ChIP-seq/CUT&RUN/CUT&Tag, and embedded post-count scRNA-seq QC.

ngssequencingbioinformaticsfastqbclrnaseqscrnaseqvariant-calling

Get set up

  1. Open Plugins in Codex and search for this plugin.
  2. Install it and complete any account authorization it asks for.
  3. Start a new thread to use it.
/plugins
Review before running
Read the installation source

Before you install

    Compatibility & limitations

    Documented for ChatGPT desktop app, Codex CLI, ChatGPT web

    Cursor: Not confirmed for Cursor.

      This listing is based on source documentation. We have not installed or runtime-tested this asset.

      How it fits together

      Requesting Code Review · SkillUse when completing tasks, implementing major features, or before merging to verify work meets requirements.Executing Plans · SkillUse when executing an implementation plan in the current session as the implementer yourself — your human partner chose inline execution, or no...Receiving Code Review · SkillUse when receiving code review feedback, before implementing suggestions, especially if feedback seems unclear or technically questionable - requires...CodeRabbit · PluginRun AI-powered code review for your current changes.

      Sources & provenance

      Reviewed 2026-09-20. Source revision: main (mutable; commit not pinned).