GeneTind-Life-Skills

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.

Ancestry decomposition PCA against the Simons Genome Diversity Project

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels

Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance

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.

Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.

Calculate polygenic risk scores from DTC genetic data using the PGS Catalog

Interact with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities.

Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.

Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages.

Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint. Use when researching disease targets, finding approved/investigational drugs, searching clinical evidence, discovering genetic associations, or analyzing compound bioactivity data.

Generate daily or on-demand medical research briefs for any medical specialty. Searches latest research from top-tier journals, delivers concise summaries with 1-sentence takeaways, images when available, and direct links. Use when user asks for medical news, research updates, journal briefs, or specialty-specific medical updates for specialties like endocrinology, cardiology, oncology, neurology, etc.

Patiently AI simplifies medical documents for patients. Takes doctor's letters, test results, prescriptions, discharge summaries, and clinical notes and explains them in clear, personalised language. Built by PharmaTools.AI.

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.

Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.

Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.

Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.

Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.

Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G predictions). Identifies genetic risk factors, prioritizes causal genes via locus-to-gene scoring, and assesses druggability. Use when asked to find genes associated with a disease or trait, discover genetic risk factors, translate GWAS signals to gene targets, or answer questions like "What genes are associated with type 2 diabetes?"

Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

Prepare for US medical licensing exams with progress tracking, weak area analysis, question bank management, and residency match planning.

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

Search and fetch structured content from Wikipedia using the MediaWiki API for reliable, encyclopedic information