fmschulz

fmschulz/omics-skills

Plugin Claude Code

Omics-focused agents and skills for Claude Code and Cowork.

fmschulz/omics-skills

Plugin Claude Code

Bioinformatics, literature discovery, scientific writing, and data visualization agents and skills for Claude Code and Cowork.

fmschulz/omics-skills

Instructions file CodexOpenCode

Instructions for fmschulz/omics-skills, covering agents.md, repository overview, default workflow selection, scientific workflow guardrails and literature-derived discovery guardrails.

fmschulz/omics-skills

Agent

Expert data visualization specialist for publication-quality figures, dashboards, and reproducible analysis notebooks.

fmschulz/omics-skills

Agent

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

fmschulz/omics-skills

Agent

Expert computational biologist for omics workflows (QC, assembly, annotation, phylogenomics, MAG recovery, viral analysis, and JGI data access).

fmschulz/omics-skills

Agent

Expert scientific writer and editor for publication-quality manuscripts, revision strategy, peer review, and reproducible methods documentation.

fmschulz/omics-skills

Skill Claude CodeCodex

Review, score, compare, and rank AI-generated biology or bioinformatics research artifacts. Use when auditing AI-scientist notebooks, code, figures, analyses, manuscripts, or reports for rigor, reproducibility, novelty, and task completion.

fmschulz/omics-skills

Skill Claude CodeCodex

Search arXiv through its official API and save local Markdown summaries. Use when finding recent CS, math, physics, or quantitative-biology preprints or resolving arXiv IDs.

fmschulz/omics-skills

Skill Claude CodeCodex

Create publication-quality static charts with matplotlib or seaborn. Use when scientific figures need readable axes, accessible palettes, tight layouts, and high data-ink design.

fmschulz/omics-skills

Skill Claude CodeCodex

Annotate genes or proteins and infer taxonomy from sequence homology. Use when assigning functions, domains, or taxonomic labels to genomes, contigs, or protein sets.

fmschulz/omics-skills

Skill Claude CodeCodex

Assemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting completeness, continuity, and contamination evidence.

fmschulz/omics-skills

Skill Claude CodeCodex

Bin and refine metagenomic contigs, then assess MAG quality. Use when recovering genomes with QuickBin and checking completeness, contamination, and bin consistency.

fmschulz/omics-skills

Skill Claude CodeCodex

Curate and validate FASTA or FAA databases. Use when standardizing headers, merging references, deduplicating sequences, converting GenBank files, or preparing BLAST, MMseqs2, and HMM inputs.

fmschulz/omics-skills

Skill Claude CodeCodex

Add schema-backed metadata validation, normalized Parquet tables, and a DuckDB catalog to a bioinformatics project. Use when an analysis needs LinkML/Pydantic records or a queryable data catalog.

fmschulz/omics-skills

Skill Claude CodeCodex

Call genes and annotate basic sequence features. Use when predicting prokaryotic, viral, or eukaryotic coding sequences before downstream annotation.

fmschulz/omics-skills

Skill Claude CodeCodex

Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.

fmschulz/omics-skills

Skill Claude CodeCodex

Evaluate scientific claims, methods, biases, and evidence strength. Use when stress-testing a study design, paper, analysis, or causal interpretation.

fmschulz/omics-skills

Skill Claude CodeCodex

Build and validate marker-gene alignments and phylogenetic trees. Use when inferring evolutionary relationships, choosing models, or checking tree support and contamination.

fmschulz/omics-skills

Skill Claude CodeCodex

Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.

fmschulz/omics-skills

Skill Claude CodeCodex

Cluster proteins into orthogroups and build pangenome matrices. Use when comparing gene-family presence, absence, expansion, contraction, or core and accessory content across genomes.

fmschulz/omics-skills

Skill Claude CodeCodex

Ingest, quality-control, and map sequencing reads with reproducible outputs. Use when processing raw reads, removing contaminants, or calculating mapping and coverage statistics.

fmschulz/omics-skills

Skill Claude CodeCodex

Analyze biological results with statistics or machine learning and produce validated reports. Use when aggregating features, testing hypotheses, training models, or reporting performance.

fmschulz/omics-skills

Skill Claude CodeCodex

Predict protein structures and perform structure-based annotation. Use when sequence evidence is insufficient or structural similarity, confidence, domains, or complexes matter.