zja2004/BGI-CLI - 第 9 页

clinpgx

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

原文语言：英语

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.

原文语言：英语

cobrapy

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

原文语言：英语

convergence-study

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

原文语言：英语

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.

原文语言：英语

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,…

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

deepchem

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

原文语言：英语

deeptools

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

原文语言：英语

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…

原文语言：英语

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.

原文语言：英语

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.

原文语言：英语

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.

原文语言：英语

drug-photo

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

原文语言：英语

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…

原文语言：英语

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。

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.

原文语言：英语

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.

原文语言：英语

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…

原文语言：英语

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.

原文语言：英语

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,…

原文语言：英语

etetoolkit

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

原文语言：英语

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…

原文语言：英语

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.

原文语言：英语

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.

原文语言：英语

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.

原文语言：英语

galaxy-bridge

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

原文语言：英语

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.

原文语言：英语

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…

原文语言：英语

genome-compare

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

原文语言：英语

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.

原文语言：英语

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,…

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

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.

原文语言：英语

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…

原文语言：英语