Skill Claude CodeCodex
Detect, quality-control, and classify viral contigs. Use when identifying viruses in assemblies, checking viral completeness and contamination, or assigning viral taxonomy.
Skill Claude CodeCodex
Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.
Skill Claude CodeCodex
Structure reproducible bioinformatics projects with canonical layouts, restartable drivers, pinned environments, provenance, and lab notebooks. Use when starting or reorganizing a genomics project or making a sequencing analysis rerunnable.
Skill Claude CodeCodex
Search bioRxiv through its official API and filter title, abstract, and author metadata. Use when finding recent biology preprints, scanning date ranges, resolving DOIs, or building author shortlists.
Skill Claude CodeCodex
Query Crossref for DOI validation, title matching, citation metadata, and bibliography audits. Use when resolving references or cleaning citation records.
Skill Claude CodeCodex
Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.
Skill Claude CodeCodex
Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.
Skill Claude CodeCodex
Query JGI Lakehouse metadata and retrieve JGI genome or read files. Use when linking GOLD, IMG, MycoCosm, Phytozome, PMO, or JAMO identifiers and datasets.
Skill Claude CodeCodex
Run a multi-agent manuscript critique with specialist reports, disagreement checks, and editor synthesis. Use for scientific review, revision assessment, or judging whether an author response resolves prior concerns.
Skill Claude CodeCodex
Author, execute, validate, and convert reproducible marimo or Jupyter notebooks. Use when delivering an analysis notebook with all cells run and figures embedded.
Skill Claude CodeCodex
Convert PDFs and office documents to clean Markdown, with structured bundles for scientific papers. Use when extracting article structure, preparing a manuscript for analysis, or creating CSAG input.
Skill Claude CodeCodex
Build production-ready Plotly Dash dashboards. Use when scientific data needs an interactive, consistently themed layout with clear and performant callbacks.
Skill Claude CodeCodex
Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.
Skill Claude CodeCodex
Produce structured, decision-ready reviews of AI/ML, computational-biology, or bioscience proposals. Use when evaluating grants, projects, or funding applications.
Skill Claude CodeCodex
Fetch bounded JSON records from UniProt, NCBI Entrez, NCBI Datasets, MGnify, InterPro, AlphaFold DB, STRING, or ENA over HTTP GET. Use when looking up an accession, taxon, entry, or structure record from a public database.
Skill Claude CodeCodex
Assess research reach with OpenAlex citations, optional Altmetric data, and journal context. Use when comparing papers, journals, or literature shortlists by influence.
Skill Claude CodeCodex
Draft, review, and revise scientific manuscripts with grounded multi-agent checks. Use when writing sections, rebuttals, response letters, manuscript QA, or sentence-level reviews.
Skill Claude CodeCodex
Track taxonomy changes and triage sequence assignments across NCBI, GTDB, ICTV, and eukaryotic frameworks. Use when comparing releases, resolving renamed taxa, or routing genomes, bins, and contigs by domain.