Skills
Design and save structured content models
This skill guides the definition and evolution of Contentrain model schemas, enabling developers to safely create singletons, collections, documents, or dictionaries. It ensures adherence to best practices for field definition, internationa…
Initialise Contentrain Content Infrastructure
Automates the setup of Contentrain content infrastructure by detecting the existing tech stack, configuring locales and domains, and scaffolding initial models. It also configures agent rules for Claude Code or Cursor and analyses the proje…
Genomic coordinate liftover and assembly conversion guide
This skill provides a comprehensive workflow for safely converting genomic coordinates between different assembly versions (e.g., hg19 to hg38). It guides the use of industry-standard tools like UCSC liftOver and CrossMap, ensuring full pro…
JASPAR Motif Analysis for ChIP-seq Validation
This skill guides the validation and enrichment analysis of transcription factor binding motifs within ENCODE ChIP-seq peaks. It leverages JASPAR's curated Position Weight Matrices (PWMs) to identify co-factors and confirm the specificity o…
ENCODE Multi-omic Data Integration
Provides a framework for planning and executing integrative analyses across multiple ENCODE experiments, including multi-omic and cross-sample workflows. It assists with compatibility verification, integration strategy selection, and the re…
Generate typed Contentrain SDK client
This skill automates the generation of a typed query SDK client from existing model definitions and content files. It executes the necessary codegen steps, updating package imports and ensuring the client is ready for use across various Jav…
Diagnose Contentrain project health issues
This skill runs comprehensive health checks across a Contentrain project, identifying structural inconsistencies, configuration errors, and stale components. It then provides a prioritized, actionable remediation plan to restore project int…
Review Content Diffs in Contentrain Branches
Inspect and evaluate pending Contentrain branches to facilitate merging, rejecting, or deferring changes. It enables developers to review patch outputs and verify file-level modifications within the branch workflow.
Aggregate histone mark peaks across multiple studies
This skill constructs comprehensive histone mark maps by aggregating narrowPeak data from multiple ENCODE experiments, donors, and labs into a single union peak set. It handles complex data quality steps, including ENCODE blocklist filterin…
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…
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…
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…