Topic · Data and Research
Bioinformatics and Genomics skills for Claude Code and Codex
Skills for genomics and molecular biology: single-cell analysis with Scanpy, scVI and AnnData, bulk RNA-seq and differential expression, variant and genomic interval tools, phylogenetics, CRISPR screens, protein structure and design with OpenFold, ESM, ProteinMPNN and RFDiffusion, Nextflow and Parabricks pipelines, and public databases such as CELLxGENE, DepMap and 1000 Genomes. They give an agent the procedures a computational biology lab follows.
Highest-scoring bioinformatics skills in the October 22, 2026 snapshot: onekgpd from K-Dense-AI/claude-scientific-skills (87/100). Scores come from the Suede Skill Check.
- 59 listed skills
- 2 repositories
- 2 with full pages
10 from official publishers. 37 bundle scripts. 21 connect to an outside service. Listed in Science and Research (59).
All 59 bioinformatics skills
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| Skill | Repository | What it does |
|---|---|---|
| onekgpd 87/100 · B | K-Dense-AI/claude-scientific-skills | Queries the 1000 Genomes Project dataset to find which individuals carry specific variants, return variants with allele frequencies, and check relatedness between individuals. |
| primer-design 87/100 · B | K-Dense-AI/claude-scientific-skills | Designs and audits PCR and RT-qPCR primers with Primer3, including off-target amplification searches, existing primer checks, and in-silico PCR and BLAST screening. |
| 13c-metabolic-flux 87/100 · B | K-Dense-AI/claude-scientific-skills | Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope… |
| adaptyv 77/100 · C | K-Dense-AI/claude-scientific-skills | Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory… |
| alphagenome 87/100 · B | K-Dense-AI/claude-scientific-skills | Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus… |
| anndata 79/100 · C | K-Dense-AI/claude-scientific-skills | Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format… |
| arboreto 87/100 · B | K-Dense-AI/claude-scientific-skills | Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for… |
| benchling-integration 87/100 · B | K-Dense-AI/claude-scientific-skills | Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries… |
| biopython 79/100 · C | K-Dense-AI/claude-scientific-skills | Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access… |
| bioservices 81/100 · B | K-Dense-AI/claude-scientific-skills | Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database… |
| bulk-rnaseq 87/100 · B | K-Dense-AI/claude-scientific-skills | Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone… |
| cellxgene-census 87/100 · B | K-Dense-AI/claude-scientific-skills | Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need… |
| cobrapy 79/100 · C | K-Dense-AI/claude-scientific-skills | Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production… |
| deepspot-m 79/100 · C | K-Dense-AI/claude-scientific-skills | Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from… |
| deeptools 81/100 · B | K-Dense-AI/claude-scientific-skills | NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq… |
| depmap 79/100 · C | K-Dense-AI/claude-scientific-skills | Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics… |
| diffdock 89/100 · B | K-Dense-AI/claude-scientific-skills | Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose… |
| diffdock-nim 74/100 · C | NVIDIA/skills | Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for DiffDock, molecular docking… |
| dnanexus-integration 79/100 · C | K-Dense-AI/claude-scientific-skills | Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow… |
| esm 79/100 · C | K-Dense-AI/claude-scientific-skills | Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and… |
| etetoolkit 81/100 · B | K-Dense-AI/claude-scientific-skills | Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O… |
| evo2-nim 79/100 · C | NVIDIA/skills | Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation, genomic sequence generation… |
| flowio 89/100 · B | K-Dense-AI/claude-scientific-skills | Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel… |
| flowkit 87/100 · B | K-Dense-AI/claude-scientific-skills | Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML… |
| folklore-variant-evidence 77/100 · C | K-Dense-AI/claude-scientific-skills | Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one… |
| geniml 81/100 · B | K-Dense-AI/claude-scientific-skills | Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect… |
| genomic-coordinates 80/100 · B | K-Dense-AI/claude-scientific-skills | Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming… |
| genomic-intelligence 80/100 · B | K-Dense-AI/claude-scientific-skills | Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language… |
| genomics-workflow-acceleration 77/100 · C | NVIDIA/skills | Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs… |
| gget 81/100 · B | K-Dense-AI/claude-scientific-skills | Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF… |
| glycoengineering 87/100 · B | K-Dense-AI/claude-scientific-skills | Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan… |
| gtars 81/100 · B | K-Dense-AI/claude-scientific-skills | Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing… |
| lamindb 85/100 · B | K-Dense-AI/claude-scientific-skills | Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology… |
| latchbio-integration 89/100 · B | K-Dense-AI/claude-scientific-skills | Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake… |
| mageck 87/100 · B | K-Dense-AI/claude-scientific-skills | Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and… |
| msa-search-nim 79/100 · C | NVIDIA/skills | Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold… |
| msa-structure-prediction-pipeline 68/100 · D | NVIDIA/skills | NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs (health.api.nvidia.com) on every call… |
| nextflow 85/100 · B | K-Dense-AI/claude-scientific-skills | Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config… |
| openfold2-nim 77/100 · C | NVIDIA/skills | Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke whenever the user mentions… |
| openfold3-nim 77/100 · C | NVIDIA/skills | Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke whenever the user mentions OpenFold3… |
| pacsomatic 87/100 · B | K-Dense-AI/claude-scientific-skills | Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet… |
| parabricks 75/100 · C | NVIDIA/skills | Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools, including planning-only questions. |
| pathogen-variant-surveillance 89/100 · B | K-Dense-AI/claude-scientific-skills | Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting… |
| pathway-enrichment 86/100 · B | K-Dense-AI/claude-scientific-skills | Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of… |
| phylogenetics 79/100 · C | K-Dense-AI/claude-scientific-skills | Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and… |
| polars-bio 87/100 · B | K-Dense-AI/claude-scientific-skills | Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF… |
| proteinmpnn-nim 79/100 · C | NVIDIA/skills | Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided PDB files and design… |
| pydeseq2 89/100 · B | K-Dense-AI/claude-scientific-skills | Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests… |
| pysam 81/100 · B | K-Dense-AI/claude-scientific-skills | Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix… |
| qiime2-amplicon 79/100 · C | K-Dense-AI/claude-scientific-skills | Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer… |
| rfdiffusion-nim 77/100 · C | NVIDIA/skills | Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues… |
| scanpy 79/100 · C | K-Dense-AI/claude-scientific-skills | Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk… |
| scikit-bio 79/100 · C | K-Dense-AI/claude-scientific-skills | Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA… |
| scvelo 87/100 · B | K-Dense-AI/claude-scientific-skills | Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or dynamical models, examines gene… |
| scvi-tools 85/100 · B | K-Dense-AI/claude-scientific-skills | Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC… |
| tellurium 87/100 · B | K-Dense-AI/claude-scientific-skills | Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter… |
| tiledbvcf 85/100 · B | K-Dense-AI/claude-scientific-skills | Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample… |
| torchdrug 87/100 · B | K-Dense-AI/claude-scientific-skills | Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation… |
| waypoint-bio 79/100 · C | K-Dense-AI/claude-scientific-skills | Supports work with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas… |
How to choose bioinformatics skills
Most skills wrap one library or database. Choose by the tool your lab already uses, since the skill encodes that tool's file formats and defaults.
NVIDIA NIM skills (OpenFold, ProteinMPNN, RFDiffusion, Evo 2, MSA search) send sequences to NVIDIA-hosted endpoints and read an NGC API key. Several state this at the top of their description; check it against your data policy.
Pipelines such as Nextflow, Parabricks and DNAnexus run long jobs on compute you pay for. Start with a small sample and confirm outputs before a full run.
Related topics
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