fmschulz/omics-skills Skills

Browser automation via agent-browser CLI for web navigation, form filling, screenshots, scraping, login flows, and UI testing.

Create publication-quality matplotlib/seaborn charts with readable axes, tight layout, and curated palettes.

Functional annotation and taxonomy inference from sequence homology.

Assemble genomes/metagenomes and produce assembly QC artifacts.

Perform metagenomic binning, refinement, and QC with completeness/contamination checks.

Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.

Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.

Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.

Build marker gene alignments and phylogenetic trees.

Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.

Cluster proteins into orthogroups and derive pangenome matrices.

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

Aggregate results, train ML models, and produce reports with validated references.

Structure prediction and structure-based annotation.

Detect, classify, and QC viral contigs.

Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.

Query JGI Lakehouse (Dremio) for genomics metadata across GOLD/IMG/Mycocosm/Phytozome and download genome files via IMG taxon OIDs.

Create/refactor reproducible analysis notebooks with Marimo (preferred) or Jupyter (minimal support). Use for interactive, narrative-first analyses.

Build production-ready Plotly Dash dashboards with consistent theming, clear layouts, and performant callbacks.