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.
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.
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.
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.
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.
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.
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.
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.
Skill Claude CodeCodex
Call genes and annotate basic sequence features. Use when predicting prokaryotic, viral, or eukaryotic coding sequences before downstream annotation.
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.
Skill Claude CodeCodex
Evaluate scientific claims, methods, biases, and evidence strength. Use when stress-testing a study design, paper, analysis, or causal interpretation.
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.
Skill Claude CodeCodex
Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.
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.
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.
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.
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.
Skill Claude CodeCodex
Detect, quality-control, and classify viral contigs. Use when identifying viruses in assemblies, checking viral completeness and contamination, or assigning viral taxonomy.
Skill Claude CodeCodex
Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.
Skill Claude CodeCodex
Structure reproducible bioinformatics projects with canonical layouts, restartable drivers, pinned environments, provenance, and lab notebooks. Use when starting or reorganizing a genomics project or making a sequencing analysis rerunnable.
Skill Claude CodeCodex
Search bioRxiv through its official API and filter title, abstract, and author metadata. Use when finding recent biology preprints, scanning date ranges, resolving DOIs, or building author shortlists.
Skill Claude CodeCodex
Query Crossref for DOI validation, title matching, citation metadata, and bibliography audits. Use when resolving references or cleaning citation records.
Skill Claude CodeCodex
Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.
Skill Claude CodeCodex
Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.