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Aggregate Hi-C Chromatin Loop Catalogs
This tool facilitates the construction of comprehensive chromatin loop catalogs by merging paired-end Hi-C loop calls (BEDPE) from disparate ENCODE experiments. It manages critical steps such as resolution harmonization, quality filtering, …
Manage Contentrain Content Entries
Automate the creation and management of content entries for existing Contentrain models, including collections, singletons, and documents. The skill enforces project-specific vocabulary, SEO best practices, and internationalisation requirem…
gwas-encode integration for functional variant annotation
This skill facilitates the intersection of genome-wide association study variants with ENCODE's functional regulatory elements. It helps developers prioritise candidate causal mechanisms by identifying which disease-associated SNPs overlap …
NCBI GEO and ENCODE Connector
Facilitates searching, querying, and cross-referencing NCBI GEO datasets with ENCODE experiments to identify complementary epigenomic data. It supports retrieving metadata, series matrices, and supplementary files via E-utilities and FTP.
Perform bulk content operations on Contentrain
This skill facilitates safe, batch operations on existing content entries, allowing developers to copy locales, update metadata status, or delete multiple entries across various models. It is designed for large-scale content management task…
Validate Regulatory Elements with GTEx Expression
This skill facilitates the integration of GTEx tissue expression data with ENCODE regulatory element findings, allowing developers to validate enhancer-gene links and assess tissue-specific gene activity. It enables the correlation of predi…
Type-safe content querying for Contentrain data
This SDK provides a type-safe, Prisma-pattern client for accessing Contentrain content across collections, singletons, dictionaries, and documents. It supports both synchronous local querying and asynchronous CDN fetching for robust data in…
Annotate regulatory variants with population genetics
This tool facilitates the annotation of ENCODE regulatory variants by querying gnomAD for population allele frequencies and gene constraint scores (pLI, LOEUF). It enables developers to prioritize variants by assessing rarity and functional…
Analyze ENCODE functional regulatory element screens
This skill facilitates the discovery and interpretation of functional regulatory elements by processing data from ENCODE's CRISPR, MPRA, and STARR-seq assays. It enables the integration of functional validation results with standard epigeno…
Comprehensive Epigenomic Profiling with ENCODE
Assemble comprehensive epigenomic profiles for specific tissues or cell types by systematically gathering histone modifications, chromatin accessibility, and DNA methylation data from ENCODE. It enables the characterisation of chromatin sta…
Real-time collaboration rooms for AI agents
This tool provides a structured interface for AI agents to interact within a real-time, multi-agent collaboration environment. Agents can join rooms, send broadcast or direct messages, and manage message history and room metadata for coordi…
Ensembl API for Variant and Gene Annotation
This tool interfaces with the Ensembl REST API to perform comprehensive genomic annotations, including variant consequence prediction (VEP), regulatory feature overlap, and coordinate liftover between assemblies. It also facilitates gene ID…
Downloading ENCODE Genomics Data Files
Facilitates the automated retrieval and organisation of ENCODE genomics files, such as BED, FASTQ, and BAM, to a local filesystem. Supports batch processing with MD5 verification and configurable directory structures based on experiment or …
Functional Genomics for Disease Mechanism Research
This skill facilitates comprehensive disease research by connecting genetic association data (GWAS) with functional genomics data from ENCODE. It annotates disease-associated loci, identifies regulatory elements, and cross-references findin…
Cross-reference ENCODE with scientific databases
Link ENCODE genomic data to external scientific databases such as PubMed, ClinicalTrials.gov, and Open Targets. This skill facilitates building translational pipelines by connecting regulatory elements to clinical research and variant annot…
Comprehensive Genomics Provenance Tracking
This skill establishes a rigorous audit trail for genomic analyses, logging every operation—including tool versions, parameters, and environment details—to ensure absolute reproducibility. It structures the data to auto-generate publication…
Annotating ENCODE Regulatory Variants with ClinVar
Cross-reference ENCODE functional genomic elements with ClinVar clinical variant classifications to identify pathogenic variants in regulatory regions. This skill enables both forward annotation of ENCODE peaks and reverse analysis of ClinV…
Comparing ENCODE data across multiple biosamples
This skill facilitates the systematic comparison of epigenomic data across diverse tissues and cell lines to distinguish constitutive regulatory elements from tissue-specific patterns. It accounts for biosample hierarchy, batch effects, and…
Generate ENCODE data citations and bibliography
This skill guides the generation of comprehensive and compliant citations for ENCODE data, covering publications, grants, and supplementary materials. It assists developers in creating accurate bibliography entries and data availability sta…
Persistent Memory for AI Coding Agents
Provides a persistent memory layer for AI coding agents, enabling semantic search, task checkpointing, and cross-session context retention. It operates locally using CPU-only embeddings and integrates with MCP-compatible clients.
Deconvolve Bulk Genomics with Single-Cell Context
This tool provides programmatic access to the CellxGene Census, enabling developers to bridge bulk ENCODE functional genomics data with cell-type-specific expression profiles. It allows for the deconvolution of broad regulatory signals by q…
Setup reproducible bioinformatics environments for ENCODE
This skill provisions fully reproducible, version-pinned conda environments and associated scripts for comprehensive ENCODE data analysis. It manages dependencies across multiple modalities (RNA-seq, ChIP-seq, ATAC-seq) using tools like STA…
Persistent memory for AI coding agents
This tool provides persistent, queryable memory for AI agents, allowing them to store critical decisions, user preferences, and lessons learned. It uses a hybrid retrieval architecture (vector similarity and full-text search) to ensure agen…
Systematic ENCODE Batch Analysis and QC Toolkit
This tool facilitates systematic, large-scale batch operations across multiple ENCODE experiments. It guides users through quality control screening, comparison table generation, and bulk data downloading using established ENCODE metrics an…