2,257 skills found · Page 65 of 76
jaechang-hits / encode-databaseENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene.
jaechang-hits / ensembl-databaseEnsembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
jaechang-hits / gnomad-databasegnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants.
jaechang-hits / gwas-databaseNHGRI-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.
jaechang-hits / jaspar-databaseJASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis.
jaechang-hits / kegg-databaseKEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
jaechang-hits / monarch-databaseMonarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking.
jaechang-hits / mouse-phenome-databaseRetrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nome…
jaechang-hits / quickgo-databaseQuery 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.
jaechang-hits / regulomedb-databaseQuery 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).
jaechang-hits / remap-databaseQuery 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.
jaechang-hits / ucsc-genome-browserQuery 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.
jaechang-hits / kegg-pathway-analysisGuide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling with offline fallbacks, cross-condition comparisons, and answer-first reporting. Consult when running enrichment with clusterProfiler or gseapy.
giuseppe-trisciuoglio / spring-boot-project-creatorCreates and scaffolds a new Spring Boot project (3.x or 4.x) by downloading from Spring Initializr, generating package structure (DDD or Layered architecture), configuring JPA, SpringDoc OpenAPI, and Docker Compose services (PostgreSQL, Redis, MongoDB)
giuseppe-trisciuoglio / aws-cloudformation-lambdaProvides AWS CloudFormation patterns for Lambda functions, layers, API Gateway integration, event sources, cold start optimization, monitoring, logging, template validation, and deployment workflows
giuseppe-trisciuoglio / langchain4j-tool-function-calling-patternsProvides and generates LangChain4j tool and function calling patterns: annotates methods as tools with @Tool, configures tool executors, registers tools with AiServices, validates tool parameters, and handles tool execution errors
giuseppe-trisciuoglio / spring-boot-crud-patternsProvides and generates complete CRUD workflows for Spring Boot 3 services. Creates feature-focused architecture with Spring Data JPA aggregates, repositories, DTOs, controllers, and REST APIs. Validates domain invariants and transaction boundaries
giuseppe-trisciuoglio / spring-boot-openapi-documentationProvides patterns to generate comprehensive REST API documentation using SpringDoc OpenAPI 3.0 and Swagger UI in Spring Boot 3.x applications
giuseppe-trisciuoglio / unit-test-controller-layerProvides patterns for unit testing REST controllers using MockMvc and @WebMvcTest. Generates controller tests that validates request/response mapping, validation, exception handling, and HTTP status codes
giuseppe-trisciuoglio / aws-lambda-php-integrationProvides AWS Lambda integration patterns for PHP with Symfony using the Bref framework. Creates Lambda handler classes, configures runtime layers, sets up SQS/SNS event triggers, implements warm-up strategies, and optimizes cold starts
giuseppe-trisciuoglio / nextjs-code-reviewProvides comprehensive code review capability for Next.js applications, validates Server Components, Client Components, Server Actions, caching strategies, metadata, API routes, middleware, and performance patterns
giuseppe-trisciuoglio / typescript-docsGenerates comprehensive TypeScript documentation using JSDoc, TypeDoc, and multi-layered documentation patterns for different audiences
giuseppe-trisciuoglio / zod-validation-utilitiesCreates reusable Zod v4 schemas, validates API payloads, forms, and configuration input, transforms and coerces data safely, and handles validation errors with strong type inference for TypeScript applications
giuseppe-trisciuoglio / unit-test-exception-handlerProvides patterns for unit testing `@ExceptionHandler` and `@ControllerAdvice` in Spring Boot applications. Validates error response formatting, mocks exceptions, verifies HTTP status codes, tests field-level validation errors, and asserts custom error payloads
giuseppe-trisciuoglio / aws-lambda-java-integrationProvides AWS Lambda integration patterns for Java with cold start optimization
giuseppe-trisciuoglio / spring-boot-rest-api-standardsProvides REST API design standards and best practices for Spring Boot projects
giuseppe-trisciuoglio / wiremock-standalone-dockerProvides patterns and configurations for running WireMock as a standalone Docker container. Generates mock HTTP endpoints, creates stub mappings for testing, validates integration scenarios, and simulates error conditions
giuseppe-trisciuoglio / aws-lambda-python-integrationProvides AWS Lambda integration patterns for Python with cold start optimization
giuseppe-trisciuoglio / aws-lambda-typescript-integrationProvides AWS Lambda integration patterns for TypeScript with cold start optimization
giuseppe-trisciuoglio / nestjsProvides comprehensive NestJS framework patterns with Drizzle ORM integration for building scalable server-side applications. Generates REST/GraphQL APIs, implements authentication guards, creates database schemas, and sets up microservices
