Skill Claude CodeCodex
Ancestry decomposition PCA against the Simons Genome Diversity Project.
22 5mo ago A 20 tokens
original MIT
Skill Claude CodeCodex
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
22 5mo ago A 34 tokens
original MIT
Skill Claude CodeCodex
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
22 5mo ago A 45 tokens
copy · 89% MIT
Skill Claude CodeCodex
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
22 5mo ago A 45 tokens
copy · 100% MIT
Skill Claude CodeCodex
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
22 5mo ago A 39 tokens
copy · 100% MIT
Skill Claude CodeCodex
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
22 5mo ago A 45 tokens
copy · 100% MIT
Skill Claude CodeCodex
Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.
22 5mo ago A 43 tokens
original MIT
Skill Claude CodeCodex
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
22 5mo ago A 50 tokens
original MIT
Skill Claude CodeCodex
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
22 5mo ago A 60 tokens
original MIT
Skill Claude CodeCodex
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
22 5mo ago A 54 tokens
copy · 100% MIT
Skill Claude CodeCodex
Automated cell behavior analysis from microscopy or XR lab recordings. Classifies cell motion phenotypes (migration, proliferation, apoptosis, division, quiescence), computes population-level quantitative metrics (growth rate, migration velocity, directionality index), and emits structured JSON for downstream…
22 5mo ago A 69 tokens
original MIT
anndata
12Skill Claude CodeCodex
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
22 5mo ago A 63 tokens
copy · 84% MIT
arboreto
13Skill Claude CodeCodex
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for…
22 5mo ago A 66 tokens
copy · 100% MIT
Skill Claude CodeCodex
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
22 5mo ago A 44 tokens
copy · 84% MIT
Skill Claude CodeCodex
Computational biology and genomics analysis pipelines. GENERAL: not locked to any specific tool — use Scanpy, Seurat, DESeq2, or any appropriate package.
22 5mo ago A 0 tokens
copy · 100% MIT
biomni
16Skill Claude CodeCodex
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation…
22 5mo ago A 82 tokens
copy · 100% MIT
biopython
17Skill Claude CodeCodex
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use…
22 5mo ago A 76 tokens
copy · 80% MIT
Skill Claude CodeCodex
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
22 5mo ago A 43 tokens
copy · 100% MIT
Skill Claude CodeCodex
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
22 5mo ago A 67 tokens
copy · 89% MIT
Skill Claude CodeCodex
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
22 5mo ago A 45 tokens
copy · 91% MIT
cobrapy
21Skill Claude CodeCodex
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
22 5mo ago A 38 tokens
copy · 84% MIT
deeptools
22Skill Claude CodeCodex
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
22 5mo ago A 51 tokens
copy · 92% MIT
Skill Claude CodeCodex
Detects common wet-lab procedural and safety errors from XR or fixed-camera lab video. Identifies pipette volume deviations, forgotten reagent additions, uncapped tubes, contamination risks, sample mix-ups, and other observable hazards. Outputs structured JSON with error type, timestamp, severity, and corrective…
22 5mo ago A 77 tokens
original MIT
Skill Claude CodeCodex
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
22 5mo ago A 49 tokens
copy · 88% MIT