Tag: genomics
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…
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…
Aggregate comprehensive open chromatin accessibility maps
This skill builds a comprehensive union map of open chromatin regions by aggregating and merging ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments. It handles cross-platform variation, applies necessary filtering (su…
Query UCSC Genome Browser REST API
Programmatically access the UCSC Genome Browser REST API to retrieve comprehensive genomic data, including cCRE annotations, TF binding clusters, and DNA sequences for any specified locus. This tool facilitates cross-referencing ENCODE data…
ENCODE Single-Cell Genomics Data Analysis Guide
This skill guides the retrieval and analysis of single-cell genomics data (scRNA-seq and scATAC-seq) from ENCODE. It covers data structure, quality control metrics, and best practices for integrating single-cell profiles with bulk epigenomi…
Searching and Exploring ENCODE Genomics Data
Provides a structured strategy for searching and exploring ENCODE Project genomics data using facets and metadata. It facilitates the discovery of experiments, files, and specific biological parameters like assays, organs, and cell lines.
Configure and connect to ENCODE Project data
This skill guides users through the installation, configuration, and authentication process for the ENCODE Toolkit MCP server. It ensures the local environment is correctly connected to the ENCODE Project genomics database for subsequent da…
Characterise Regulatory Elements with ENCODE Data
Identify and characterise candidate cis-regulatory elements using ENCODE datasets and the cCRE catalog. The skill enables the discovery of active enhancers, promoter state mapping, and super-enhancer identification using ChromHMM and ROSE.
Generate scientific text from ENCODE provenance
This skill auto-generates publication-ready scientific documentation, including methods sections and figure legends, by rigorously compiling experimental and computational metadata from ENCODE provenance records. It ensures adherence to hig…
ENCODE Hi-C Processing Pipeline
Executes the ENCODE Hi-C pipeline using Nextflow to transform FASTQ files into multi-resolution contact matrices and loop calls. The pipeline supports local, SLURM, and cloud-based deployments via Docker.
CUT and CUT Processing Pipeline
Executes a Nextflow-based pipeline for processing CUT and CUT data from FASTQ files to peaks and signal tracks. The workflow incorporates spike-in normalisation and SEACR peak calling for high-resolution chromatin profiling.
ENCODE ChIP-seq Processing Pipeline
This Nextflow-based pipeline executes the complete ENCODE ChIP-seq processing workflow, transforming raw FASTQ files into peaks and signal tracks. It handles quality control, alignment, peak calling with MACS2, and IDR analysis using Docker…
Aggregate DNA Methylation Across ENCODE Studies
Build comprehensive tissue-level DNA methylation landscapes by aggregating WGBS data from multiple ENCODE experiments. The skill handles quality-gating, coverage filtering, and the identification of hypomethylated regions and partially meth…
Integrating JASPAR Motifs with ENCODE ChIP-seq
Integrate JASPAR transcription factor binding profiles with ENCODE ChIP-seq peaks to validate binding targets and discover co-factors. This skill enables scanning regulatory regions for motif enrichment and assessing the impact of genomic v…
Aggregate Hi-C Chromatin Contact Maps
Aggregates BEDPE loop calls from multiple ENCODE Hi-C experiments to create a comprehensive union catalog of chromatin contacts. It performs resolution-aware anchor matching, quality-gating, and filtering against the ENCODE blacklist.
Aggregate Histone ChIP-seq Peaks Across Studies
This skill aggregates histone ChIP-seq peaks from multiple ENCODE experiments into a unified, confidence-annotated map. It manages cross-lab batch effects and applies rigorous filtering, including ENCODE blocklist removal and signal value q…
Integrating GTEx Expression with ENCODE Data
This skill enables the integration of GTEx tissue expression data with ENCODE regulatory elements to validate enhancer-gene links and assess tissue-specific activity. It facilitates querying median TPM, eQTLs, and transcript-level expressio…
NCBI GEO and ENCODE Data Connector
Search, query, and cross-reference NCBI GEO datasets with ENCODE experiments to identify complementary genomic data. The skill facilitates downloading metadata, series matrices, and supplementary files while enabling the linking of GEO acce…
Analyze ENCODE functional genomics screens
This skill processes and interprets functional genomics data from ENCODE, including CRISPR screens, MPRA, and STARR-seq. It helps developers validate candidate regulatory elements and integrate functional activity data with standard epigeno…
Ensembl Genomic Annotation and VEP Skill
Query the Ensembl REST API to perform variant effect prediction (VEP), coordinate liftover between assemblies, and retrieve regulatory feature annotations. The skill also facilitates gene identifier resolution and phenotype association look…
ENCODE Genomics Data Downloader and Manager
This tool facilitates the programmatic retrieval of diverse ENCODE genomics files, supporting both specific accession downloads and comprehensive batch operations. It includes advanced features such as dry-run previews, MD5 verification, an…
Disease Research with ENCODE Functional Genomics
This skill enables researchers to investigate disease mechanisms by connecting GWAS variants to ENCODE regulatory elements and functional genomics data. It integrates ENCODE annotations with Open Targets, PubMed, and ClinicalTrials.gov to i…
Comprehensive provenance tracking for genomics analysis
This skill establishes a rigorous audit trail for genomic data processing, logging every tool version, parameter, and reference file used. It ensures complete reproducibility by generating detailed, publication-ready methods sections from t…
Cross-reference ENCODE data with scientific databases
This skill facilitates the comprehensive cross-referencing of ENCODE genomic data with major external scientific resources. It enables the construction of translational pipelines by linking experiments to literature, clinical trials, and va…