zja2004/BGI-CLI - Página 9

clinpgx

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

Idioma do texto original: inglês

clinvar-database

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.

Idioma do texto original: inglês

cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Idioma do texto original: inglês

convergence-study

Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification

Idioma do texto original: inglês

cosmic-database

Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

Idioma do texto original: inglês

crisis-detection-intervention-ai

Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols. Implements suicide ideation detection, automated escalation, and crisis resource integration. Use for mental health apps, recovery platforms,…

Idioma do texto original: inglês

dask

Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core…

Idioma do texto original: inglês

datacommons-client

Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available…

Idioma do texto original: inglês

datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol…

Idioma do texto original: inglês

deepchem

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Idioma do texto original: inglês

deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Idioma do texto original: inglês

depmap

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology…

Idioma do texto original: inglês

diffdock

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Idioma do texto original: inglês

differentiation-schemes

Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes, building stencils, handling boundaries, estimating truncation error, or analyzing dispersion and dissipation.

Idioma do texto original: inglês

dnanexus-integration

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.

Idioma do texto original: inglês

drug-photo

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

Idioma do texto original: inglês

drugbank-database

Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug…

Idioma do texto original: inglês

emergency-card

生成紧急情况下快速访问的医疗信息摘要卡片。当用户需要旅行、就诊准备、紧急情况或询问"紧急信息"、"医疗卡片"、"急救信息"时使用此技能。提取关键信息（过敏、用药、急症、植入物），支持多格式输出（JSON、文本、二维码），用于急救或快速就医。

Idioma do texto original: chinês

ena-database

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

Idioma do texto original: inglês

ensembl-database

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

Idioma do texto original: inglês

epidemiologist-analyst

Analyzes disease patterns and health events through epidemiological lens using surveillance systems, outbreak investigation methods, and disease modeling frameworks. Provides insights on disease spread, risk factors, prevention strategies, and public health…

Idioma do texto original: inglês

equity-scorer

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.

Idioma do texto original: inglês

esm

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences,…

Idioma do texto original: inglês

etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Idioma do texto original: inglês

exploratory-data-analysis

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file…

Idioma do texto original: inglês

fastq-analysis-pipeline

Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.

Idioma do texto original: inglês

fda-database

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

Idioma do texto original: inglês

flowio

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Idioma do texto original: inglês

galaxy-bridge

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

Idioma do texto original: inglês

gene-database

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

Idioma do texto original: inglês

geniml

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based…

Idioma do texto original: inglês

genome-compare

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

Idioma do texto original: inglês

geo-database

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Idioma do texto original: inglês

geopandas

Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations,…

Idioma do texto original: inglês

gget

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use…

Idioma do texto original: inglês

ginkgo-cloud-lab

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or…

Idioma do texto original: inglês

glycoengineering

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic…

Idioma do texto original: inglês

gnomad-database

Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function…

Idioma do texto original: inglês

grief-companion

Compassionate bereavement support, memorial creation, grief education, and healing journey guidance. Specializes in understanding grief stages, creating meaningful tributes, and supporting the non-linear path of loss.

Idioma do texto original: inglês

gtars

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine…

Idioma do texto original: inglês