Loading...
Loading...
Found 69 Skills
Use when writing or modifying Python code that imports `genoray` to read genotypes/dosages from VCF, PGEN, or SparseVar (`.svar`) files. Covers the public API surface, mode constants, range queries, chunking, filtering, and the SparseVar workflow. Skip for unrelated bioinformatics work.
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
Comprehensive scientific research toolkit with 139 specialized skills for biology, chemistry, medicine, data science, and computational research. Transforms Claude into an AI research assistant with access to scientific databases, analysis tools, and domain-specific workflows.
Query the ChEMBL database for bioactive compounds, drug targets, and bioactivity data. Use this skill when searching for small molecules, finding inhibitors for protein targets, or analyzing drug mechanisms of action.
Build and run FastFold BoltzGen protein-design workflows end-to-end through API or Composer draft links. Use this whenever users mention BoltzGen, design-spec YAMLs, binder design, multi-spec scaffold workflows, CIF/PDB preparation, workflow graph upsert, `/workflow/composer/<id>`, candidate metrics/structure results, or ask naturally for "help me design a protein" / "give me a simple example".
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug interactions, and literature. Features collision-aware searches, evidence grading (T1-T4), explicit Open Targets coverage, and mandatory completeness auditing. Use when users ask about drug targets, proteins, genes, or need target validation, druggability assessment, or comprehensive target profiling.
Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.
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.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options for specific mutations (EGFR, KRAS, BRAF, etc.), therapy resistance, or clinical trial eligibility.