Skill Claude CodeCodex
Ancestry decomposition PCA against the Simons Genome Diversity Project.
not rated 22 5mo ago A 20 tokens
original MIT
22Stars on the repository
200Mods indexed here, across every type
5mo agoLast push, which is what freshness is scored on
MITLicence, which decides whether bodies are shown
Skill Claude CodeCodex
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
not rated 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.
not rated 22 5mo ago A 45 tokens
copy · 86% 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.
not rated 22 5mo ago A 45 tokens
copy · 88% 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.
not rated 22 5mo ago A 39 tokens
copy · 86% 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.
not rated 22 5mo ago A 45 tokens
copy · 84% 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.
not rated 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.
not rated 22 5mo ago A 50 tokens
copy · 92% 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.
not rated 22 5mo ago A 60 tokens
copy · 91% 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.
not rated 22 5mo ago A 54 tokens
copy · 84% 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…
not rated 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.
not rated 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…
not rated 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.
not rated 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.
not rated 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…
not rated 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…
not rated 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.
not rated 22 5mo ago A 43 tokens
copy · 89% 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.
not rated 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.
not rated 22 5mo ago A 45 tokens
copy · 89% 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.
not rated 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.
not rated 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…
not rated 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.
not rated 22 5mo ago A 49 tokens
copy · 88% MIT
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