fmschulz/omics-skills

fmschulz/omics-skills · AGENTS.md

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

fmschulz/omics-skills · skills/arxiv-search/SKILL.md · Search arXiv through its official API and save local Markdown summaries. Use when finding recent CS, math, physics, or…

fmschulz/omics-skills · skills/beautiful-data-viz/SKILL.md · Create publication-quality static charts with matplotlib or seaborn. Use when scientific figures need readable axes…

fmschulz/omics-skills · skills/bio-annotation/SKILL.md · Annotate genes or proteins and infer taxonomy from sequence homology. Use when assigning functions, domains, or…

fmschulz/omics-skills · skills/bio-assembly-qc/SKILL.md · Assemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting…

fmschulz/omics-skills · skills/bio-binning-qc/SKILL.md · Bin and refine metagenomic contigs, then assess MAG quality. Use when recovering genomes with QuickBin and checking…

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

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

fmschulz/omics-skills · skills/bio-gene-calling/SKILL.md · Predict coding sequences and screen assemblies for non-coding RNA features. Use when calling genes in prokaryotic…

fmschulz/omics-skills · skills/bio-interdomain-hgt/SKILL.md · Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when…

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

fmschulz/omics-skills · skills/bio-phylogenomics/SKILL.md · Build and validate marker-gene alignments and phylogenetic trees. Use when inferring evolutionary relationships…

fmschulz/omics-skills · skills/bio-prefect-dask-nextflow/SKILL.md · Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local…

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

fmschulz/omics-skills · skills/bio-reads-qc-mapping/SKILL.md · Ingest, quality-control, and map sequencing reads with reproducible outputs. Use when processing raw reads, removing…

fmschulz/omics-skills · skills/bio-stats-ml-reporting/SKILL.md · Analyze biological results with statistics or machine learning and produce validated reports. Use when aggregating…

fmschulz/omics-skills · skills/bio-structure-annotation/SKILL.md · Predict protein or complex structures and annotate proteins by structural similarity. Use when predicting a fold…

fmschulz/omics-skills · skills/bio-viromics/SKILL.md · Detect, quality-control, and classify viral contigs. Use when identifying viruses in assemblies, checking viral…

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 · Search bioRxiv through its official API and filter title, abstract, and author metadata. Use when finding recent…

fmschulz/omics-skills · skills/crossref-lookup/SKILL.md · Query Crossref for DOI validation, title matching, citation metadata, and bibliography audits. Use when resolving…

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 scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array…

fmschulz/omics-skills · skills/manuscript-review-council/SKILL.md · Produce a journal-style peer review of a scientific manuscript with specialist reports and an editor decision. Use when…

fmschulz/omics-skills · skills/notebooks/SKILL.md · Author, execute, validate, and convert reproducible marimo or Jupyter notebooks. Use when delivering an analysis…

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 production-ready Plotly Dash dashboards. Use when scientific data needs an interactive, consistently themed…

fmschulz/omics-skills · skills/polars-dovmed/SKILL.md · Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries…

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

fmschulz/omics-skills · skills/public-db-lookup/SKILL.md · Fetch bounded JSON records from UniProt, NCBI Entrez, NCBI Datasets, MGnify, InterPro, AlphaFold DB, STRING, or ENA…

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 edit scientific prose while preserving its claims and evidence. Use when writing manuscript sections, proposal…

fmschulz/omics-skills · skills/tracking-taxonomy-updates/SKILL.md · Track taxonomy changes and triage sequence assignments across NCBI, GTDB, ICTV, and eukaryotic frameworks. Use when…