「query skill」の検索結果

Use CloudBase document database Web SDK to query, create, update, and delete data. Supports complex queries, pagination, aggregation, and geolocation queries.

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

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Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

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Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

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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.

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Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

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Interactive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL. Use when searching documentation, managing projects/tasks, or querying indexed knowledge. Provides RAG-powered semantic search, website crawling, document upload, hierarchical project/task management, and document versioning. Always try Archon first for external documentation and knowledge retrieval before using other sources.

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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.

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Implement semantic vector search with AgentDB for intelligent document retrieval, similarity matching, and context-aware querying. Use when building RAG systems, semantic search engines, or intelligent knowledge bases.

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Analyzes Rails applications and generates comprehensive upgrade reports with breaking changes, deprecations, and step-by-step migration guides for Rails 2.3 through 8.1. Use when upgrading Rails applications, planning multi-hop upgrades, querying version-specific changes, or answering what stands between the app and the next Rails version. Based on FastRuby.io methodology and "The Complete Guide to Upgrade Rails" ebook.

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Postgres best practices maintained by Supabase, for Postgres running anywhere. Load this skill BEFORE writing or changing anything that lives in a Postgres database: creating or altering tables and columns (including choosing column types), schema design, migrations and declarative schema files, RLS policies and the tests that verify them, indexes, triggers, database functions, queues and scheduled jobs (pg_cron, pgmq), vector/semantic search (pgvector), and restoring dumps (pg_restore) or importing data. Also load it when diagnosing slow queries, high CPU, timeouts, EXPLAIN plans, connection exhaustion, locking, bloat, or rows visible to the wrong user or tenant. This is not just a performance guide — schema, migration, security, and SQL authoring tasks need these rules too, even for a one-column change or a single query.

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Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.

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Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

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Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair. Use for TF co-occupancy, regulatory annotation, and TF binding atlases. Use jaspar-database for PWM motifs; encode-database for ENCODE tracks.

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NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.

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Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.

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CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.

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Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key). For clinical pathogenicity use clinvar-database; for population frequencies use gnomad-database.

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Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores. Use for UCSC annotations; Ensembl REST API for Ensembl gene IDs and VEP variant annotation.

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Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none). Use for GWAS hit prioritization, regulatory variant annotation, cis-regulatory discovery. Use clinvar-database for pathogenicity; gwas-database for trait associations.

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Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.

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Query CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core, train PyTorch models. For your own data use scanpy; for annotated data use anndata.

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Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns ClinSig, submitter data, conditions, HGVS. For GWAS use gwas-database; for variant consequence prediction use Ensembl VEP.

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Query ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase; fetch details by NCT ID; filter by status; paginate; export CSV. For clinical research, patient matching, and trial portfolio analysis.

日本語の概要は準備中です。原文の説明を表示しています。