fmschulz/omics-skills

fmschulz/omics-skills · AGENTS.md

fmschulz/omics-skills · skills/ai-scientist-evaluator/SKILL.md · Score finished AI-generated biology or bioinformatics work against its task and required artifacts. Use when auditing…

fmschulz/omics-skills · skills/arxiv-search/SKILL.md · Search arXiv through its official API and write Markdown notes for arXiv IDs. Use for CS, math, physics, statistics, or…

fmschulz/omics-skills · skills/beautiful-data-viz/SKILL.md · Shared design rules for every plot, figure, chart, dashboard or data visual (matplotlib, seaborn, ggplot2, Plotly…

fmschulz/omics-skills · skills/bio-annotation/SKILL.md · Annotate proteins with functions, domains, and homology-based taxonomy. Use when assigning functional or taxonomic…

fmschulz/omics-skills · skills/bio-assembly-qc/SKILL.md · Assemble isolate genomes or metagenomes and run QUAST/MetaQUAST with a restartable driver. Use when turning QC-passed…

fmschulz/omics-skills · skills/bio-binning-qc/SKILL.md · Bin metagenomic contigs with QuickBin and assess MAG quality with CheckM2, GUNC, EukCC, and GTDB-Tk. Use when binning…

fmschulz/omics-skills · skills/bio-fasta-database-curator/SKILL.md · Curate and validate FASTA or FAA databases. Use when standardizing headers, merging or deduplicating references…

fmschulz/omics-skills · skills/bio-foundation-housekeeping/SKILL.md · Add LinkML/Pydantic metadata validation, Parquet tables, and a DuckDB catalog to a bioinformatics project. Use when…

fmschulz/omics-skills · skills/bio-gene-calling/SKILL.md · Predict genes and count tRNA and rRNA genes in assemblies. Use when calling CDS in prokaryotic, viral, or eukaryotic…

fmschulz/omics-skills · skills/bio-interdomain-hgt/SKILL.md · Detect and polarize interdomain horizontal gene transfer with reciprocal hits, genomic context, and gene trees. Use for…

fmschulz/omics-skills · skills/bio-logic/SKILL.md · Assess a scientific claim, study design, or interpretation against its evidence. Use when testing causal reasoning…

fmschulz/omics-skills · skills/bio-phylogenomics/SKILL.md · Build marker-gene alignments and ML trees and find closest relatives. Use when inferring phylogenies, placing genomes…

fmschulz/omics-skills · skills/bio-prefect-dask-nextflow/SKILL.md · Choose and scaffold Prefect+Dask or Nextflow pipelines. Use when designing a local, distributed, or Slurm-backed…

fmschulz/omics-skills · skills/bio-protein-clustering-pangenome/SKILL.md · Cluster proteins into orthogroups and build pangenome matrices. Use when comparing gene-family presence, copy number…

fmschulz/omics-skills · skills/bio-reads-qc-mapping/SKILL.md · QC, trim, and map short or long reads with a restartable driver. Use when processing raw FASTQ, removing adapters or…

fmschulz/omics-skills · skills/bio-stats-ml-reporting/SKILL.md · Run statistics or machine learning on biological results and write a validated report. Use when testing hypotheses…

fmschulz/omics-skills · skills/bio-structure-annotation/SKILL.md · Predict protein or complex structures and find structural homologs. Use when sequence search gives weak or no hits, or…

fmschulz/omics-skills · skills/bio-viromics/SKILL.md · Detect, QC, and classify viral contigs with geNomad, CheckV, vConTACT3, and GVClass. Use when finding viruses in…

fmschulz/omics-skills · skills/bio-workflow-methods-docwriter/SKILL.md · Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands…

fmschulz/omics-skills · skills/bioinformatics-project/SKILL.md · Structure reproducible bioinformatics projects with canonical layouts, restartable drivers, pinned environments…

fmschulz/omics-skills · skills/biorxiv-search/SKILL.md · Scan bioRxiv by date range, category, author, or DOI through its official API, with local keyword filtering. Use for…

fmschulz/omics-skills · skills/crossref-lookup/SKILL.md · Query Crossref to validate DOIs, match titles to DOIs, fetch citation metadata, and audit bibliographies. Use when…

fmschulz/omics-skills · skills/csag-extraction/SKILL.md · Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing…

fmschulz/omics-skills · skills/exploratory-data-analysis/SKILL.md · Inspect a scientific data file and report its structure and quality. Use when triaging an unknown table, array…

fmschulz/omics-skills · skills/manuscript-review-council/SKILL.md · Journal-style manuscript peer review with specialist reviewer reports and an editor decision. Use when judging…

fmschulz/omics-skills · skills/notebooks/SKILL.md · Author, run and convert marimo or Jupyter notebooks. Use when delivering an analysis notebook executed end to end with…

fmschulz/omics-skills · skills/pdf-to-md/SKILL.md · Convert PDFs and office documents to clean Markdown, with structured bundles for scientific papers. Use when extracting…

fmschulz/omics-skills · skills/plotly-dashboard-skill/SKILL.md · Build Plotly Dash apps with one shared figure template and fast callbacks. Use when data needs an interactive…

fmschulz/omics-skills · skills/polars-dovmed/SKILL.md · Run structured full-text searches of PMC Open Access and bioRxiv with polars-dovmed. Use for reproducible literature…

fmschulz/omics-skills · skills/proposal-review/SKILL.md · Review an AI/ML, computational-biology, or bioscience research proposal for a funding decision. Use when scoring a…

fmschulz/omics-skills · skills/public-db-lookup/SKILL.md · Fetch compact JSON records from UniProt, NCBI, MGnify, InterPro, AlphaFold DB, STRING, or ENA. Use when looking up an…

fmschulz/omics-skills · skills/scientific-impact-assessment/SKILL.md · Assess research reach with OpenAlex citations, optional Altmetric data, and journal context. Use when comparing papers…

fmschulz/omics-skills · skills/scientific-writing/SKILL.md · Draft or revise scientific prose without changing its claims. Use for manuscript sections, proposal narratives…

fmschulz/omics-skills · skills/tracking-taxonomy-updates/SKILL.md · Track NCBI, GTDB, ICTV, and eukaryotic taxonomy releases, and route genomes, bins, or contigs to domain classifiers…