Tag: genomics
Annotating Genetic Variants with ENCODE Data
Annotate genetic variants with ENCODE functional genomics data to identify causal regulatory elements and link them to target genes. The skill supports the full post-GWAS workflow, including tissue-specific mapping, enrichment testing, and …
Visualizing ENCODE Genomic Data Workflows
This skill guides the creation of publication-quality visualizations for ENCODE data, covering deepTools heatmaps, profile plots, and correlation analysis. It also details using IGV for interactive genome browser viewing and web embedding v…
Query Genomic Annotations from UCSC Browser API
This tool provides programmatic access to the UCSC Genome Browser REST API, enabling the retrieval of comprehensive, cross-experiment genomic annotations. Developers can query regulatory elements, TF binding clusters, and DNA sequences for …
Analyzing ENCODE single-cell genomics data
This skill guides the retrieval and analysis of single-cell genomics data (scRNA-seq and scATAC-seq) from the ENCODE project. It provides detailed protocols for data structure, quality assessment, and integrating single-cell profiles with b…
ENCODE Toolkit Setup and Configuration
Provides instructions for installing, configuring, and verifying the ENCODE Toolkit MCP server. It covers installation via uvx or pip, managing credentials, and testing connections using metadata and search queries.
Search and explore ENCODE genomics data
This skill facilitates comprehensive querying and exploration of the ENCODE Project's vast genomics dataset. It guides users through a structured, multi-phase search process, allowing them to first explore available facets, validate metadat…
generate scientific writing from provenance data
This skill auto-generates publication-ready scientific documentation, including methods sections and figure legends, directly from ENCODE analysis provenance records. It ensures rigorous reporting of all experimental and computational param…
Characterize Genomic Regulatory Elements Using ENCODE Data
This skill facilitates the discovery and classification of cis-regulatory elements (cCREs) by integrating ENCODE's comprehensive catalog with multi-omic data. It supports advanced analysis of chromatin states, identifying promoters, enhance…
Publication Trust Assessment and Reliability Check
This skill systematically assesses the scientific reliability of academic publications by checking for formal retractions, errata, and expressions of concern. It critically searches for independent contradictions and replication failures ac…
ENCODE Hi-C Data Processing Pipeline
This Nextflow pipeline processes Hi-C FASTQ files to generate multi-resolution contact matrices and chromatin loop calls. It integrates BWA, pairtools, Juicer, and cooler for end-to-end chromatin conformation analysis.
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…
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.
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…
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…
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, …
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.
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…
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 …
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…