omics-skills

Plugin omics-skills from marketplace omics-skills in fmschulz/omics-skills. Commands read from the repo's manifest — today.

Skills (12)

• beautiful-data-viz

  Shared design rules for every plot, figure, chart, dashboard or Dash app (matplotlib, seaborn, ggplot2, Plotly, HTML/SVG). Greyscale first, color only to encode information, colorblind-safe, publication-ready export. Use when making, restyling or reviewing any chart, figure or dashboard.

• bio-annotation

  Annotate proteins with functions, domains, and homology-based taxonomy. Use when assigning functional or taxonomic labels to proteins from genomes, contigs, or MAGs.

• bio-interdomain-hgt

  Detect and polarize interdomain horizontal gene transfer with reciprocal hits, genomic context, and gene trees. Use for virus-host gene exchange, endogenous viral elements, or donor direction.

• bio-logic

  Assess a scientific claim, study design, or interpretation of project results against its evidence, and keep a hypothesis register. Use when testing causal reasoning, finding bias, weighing alternative explanations, or revising hypotheses.

• bio-viromics

  Detect, QC, and classify viral contigs with geNomad, CheckV, vConTACT3, and GVClass. Use when finding viruses in assemblies, grading viral genomes, or assigning phage or giant-virus taxonomy.

• bioinformatics-project

  Structure reproducible bioinformatics projects with a canonical layout, restartable drivers, pinned environments, provenance, and lab notebook. Use when starting or reorganizing a genomics project or making a sequencing analysis rerunnable.

• crossref-lookup

  Query Crossref to validate DOIs, match titles to DOIs, fetch citation metadata and audit bibliographies; also report OpenAlex citation counts. Use when resolving references, cleaning citation records, or comparing papers by citations.

• notebooks

  Author, run and convert marimo or Jupyter notebooks. Use when delivering an analysis notebook executed end to end with figures embedded.

• omics-pipeline

  Run omics pipeline stages from reads QC and mapping to assembly, binning, gene calling, phylogenomics and structure, and open the annotation, viromics and HGT stage skills. Use when a genome, metagenome or viral analysis needs a stage page, a driver or the shared pipeline rules.

• polars-dovmed

  Run reproducible full-text searches of PMC Open Access and bioRxiv with polars-dovmed (saved query file, year bands, local parquet). Use when a literature search must be repeatable, or for a quick lookup through the hosted API.

• public-db-lookup

  Fetch compact JSON records from UniProt, NCBI, MGnify, InterPro, AlphaFold DB, STRING, or ENA. Use when looking up an accession, taxon, entry, or structure in a public database.

• tracking-taxonomy-updates

  Route genomes, bins, or contigs to domain classifiers with QuickClade, and track NCBI, GTDB, ICTV, and eukaryotic taxonomy releases. Use when assigning taxonomy, choosing a domain-specific tool, comparing releases, or resolving renamed taxa.

Subagents (1)

• literature-expert

  Literature discovery and citation metadata agent for peer-reviewed papers, preprints, DOI lookup, and evidence-grounded search triage.

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