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Translate Contentrain Content Across Locales
This skill automates the translation of Contentrain content entries into new locales while adhering to strict i18n quality, vocabulary, and string length constraints. It manages the end-to-end workflow from identifying translation gaps to v…
Validate and fix content schema issues
This skill diagnoses content validity against defined model schemas, identifying structural, type, and relational errors. It can automatically apply safe fixes and guide the user through re-validation and submission workflows.
ENCODE DNase-seq Pipeline for Hotspots and Footprints
This skill executes the comprehensive ENCODE DNase-seq pipeline, processing paired FASTQ reads to identify DNase hypersensitive sites (DHSs) and perform TF footprinting analysis. It utilizes Nextflow to generate critical data products, incl…
Launch Contentrain Local Review Interface
Launches a local web interface for visual review of content, branches, and validation results. It acts as a monitoring and approval surface for developer-led decisions on agent-driven changes.
CUT/CUT Peak Calling Pipeline
This tool executes a comprehensive Nextflow pipeline for processing CUT or CUT FASTQ data. It handles alignment, spike-in normalization, and generates peak calls using SEACR or MACS2, producing normalized signal tracks and genomic peaks.
ENCODE ChIP-seq Analysis Pipeline for Peak Calling
This skill executes a complete, standards-compliant ChIP-seq workflow, processing raw FASTQ files through alignment, MACS2 peak calling, and IDR analysis. It generates comprehensive peak sets and signal tracks, adhering to ENCODE guidelines…
Type-safe Contentrain Query SDK
A type-safe SDK for querying Contentrain content using a Prisma-pattern generated client. It supports both synchronous local data access and asynchronous remote fetching via CDN mode.
ENCODE ATAC-seq Pipeline for Chromatin Accessibility Analysis
This skill executes the comprehensive ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and filtering. It generates high-quality peak calls and signal tracks suitable for detailed chromatin acces…
ENCODE Peak Annotation and Functional Enrichment
Annotate ENCODE genomic peaks with regulatory features and nearby genes using ChIPseeker and GREAT. The workflow enables genomic feature distribution analysis and functional enrichment via clusterProfiler.
Comprehensive content quality and compliance review
This skill executes a comprehensive pre-publish audit, validating content against industry standards including SEO, accessibility, security, and i18n completeness. It generates a structured report detailing critical, warning, and informatio…
Content Quality and SEO Compliance Review
This skill enforces comprehensive content standards, covering SEO best practices, heading hierarchy, and structural integrity. It validates content against defined tone, vocabulary, and accessibility rules across various content types.
ENCODE Multi-Omics Data Integration
Integrates multiple ENCODE data types, including RNA-seq, ATAC-seq, and ChIP-seq, to construct a comprehensive regulatory landscape for specific tissues or cell types. It enables chromatin state annotation, enhancer-gene linkage, and the ch…
Codebase Normalization and Content Extraction
This skill normalizes codebases by extracting hardcoded strings into a managed content repository and subsequently patching the source files with content references. This two-phase process ensures content is centralized, translatable, and m…
Aggregate DNA Methylation Data Across Studies
Construct comprehensive tissue-level DNA methylation landscapes by aggregating WGBS data from multiple ENCODE experiments. The process includes quality-gating, coverage filtering, and the identification of hypomethylated regions and partial…
Motif discovery and enrichment analysis for peak data
This skill guides the enrichment analysis of transcription factor binding motifs in ChIP-seq and ATAC-seq peaks. It covers best practices and workflows using industry-standard suites like HOMER and MEME for both de novo and known motif disc…
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…