ammawla

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs bulk profiles. Covers platform differences (10X Chromium, Smart-seq2, Drop-seq), quality limitations of single-cell data, multimodal integration (RNA+ATAC), and cross-study reproducibility concerns. Also use for cell type annotation, gene detection limits, dropout artifacts, and single-cell data structure in ENCODE.

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Track ENCODE experiments locally with publications, citations, and provenance. Use when the user wants to build a collection of experiments, manage citations, compare experiments, or track data provenance.

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Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under peaks, query ENCODE cCREs or TF rPeak clusters from UCSC, check what tracks are available for a genome assembly, get chromatin accessibility across cell types, or cross-reference ENCODE data with UCSC-hosted annotations. Also use when the user mentions UCSC, genome browser, cCRE lookup, SCREEN, TF binding clusters, DNA sequence retrieval, or track data extraction.

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Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots. Use when users need to create visualizations of ChIP-seq signal, peak landscapes, genome browser views, or any visual representation of ENCODE data. Trigger on: heatmap, visualization, genome browser, track hub, IGV, deeptools, signal plot, peak visualization, profile plot, publication figure, bigWig visualization.

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Search and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what data is available for specific assays, organs, cell lines, or targets.

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Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak set. Handles cross-lab variation, ATAC vs DNase platform differences, and ENCODE blocklist filtering.

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Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, or generate summary reports. Trigger on: batch analysis, multiple experiments, bulk processing, experiment comparison, batch QC, multi-sample, batch download, experiment table, summary report, collection analysis.

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Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts, and Python requirements. Use when the user needs to set up a bioinformatics workstation, install tools for a specific assay, create reproducible environments, or troubleshoot dependency issues. Trigger on: install tools, set up environment, conda create, bioinformatics setup, install R packages, install Bioconductor, install pipeline tools.

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Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger on: CellxGene, single-cell atlas, cell type expression, Census, cell type specificity, single-cell context, scRNA-seq atlas.

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Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCODE data with other scientific MCP servers, or build translational pipelines from genomic data to clinical application.

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Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models, cross-reference with clinical trials and drug databases, or conduct any disease-focused, pathology-driven, or clinical variant interpretation workflow. Covers the full pipeline from disease-tissue mapping through GWAS variant annotation, heritability enrichment, cancer epigenomics, drug target identification, and clinical trial cross-referencing. Integrates ENCODE with Open Targets, PubMed, ClinicalTrials.gov, and bioRxiv.

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Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

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Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE and GEO data, find supplementary files from GEO, or link GEO series to ENCODE experiments for provenance tracking. Also use when the user mentions GEO, GSE, GSM, GPL, GDS, series matrix, SOFT format, or needs to find expression data in GEO that complements their ENCODE analysis.

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Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, genome-wide association, SNP association, trait association, GWAS Catalog, disease association, risk variant, lead SNP, LD proxy.

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Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolution-aware anchor matching, cross-lab variation, and Hi-C-specific quality metrics.

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Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data into tissue-level methylation profiles. Handles coverage filtering, identifies hypomethylated regions (HMRs) and partially methylated domains (PMDs), and manages cross-lab variation.

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Discover and characterize regulatory elements (enhancers, promoters, silencers, insulators, super-enhancers) using ENCODE data and the cCRE catalog. Use when the user wants to find candidate regulatory elements, identify active enhancers in a tissue, map promoter states, classify chromatin states with ChromHMM, identify super-enhancers with ROSE, understand the functional validation hierarchy (CRISPR > MPRA > reporter), or characterize non-coding genomic regions. Covers the full workflow from ENCODE cCRE lookup through chromatin state segmentation to functional validation and enhancer-gene linkage. Use this skill for ANY regulatory element discovery, classification, or characterization task.

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Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact on regulatory elements, perform enrichment testing of variant sets in tissue-specific annotations, or link variants to target genes through enhancer-gene maps. Handles the full post-GWAS workflow from variant set → tissue mapping → functional annotation → fine-mapping awareness → enrichment → variant-to-gene → prioritization. Use this skill for ANY variant interpretation task involving ENCODE chromatin, accessibility, TF binding, or 3D genome data.

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Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinical significance, pathogenic variant, variant classification, clinical variant, disease variant, VUS, benign, likely pathogenic.

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Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a gene is expressed in a tissue, correlate regulatory elements with expression, or validate ENCODE findings against GTEx. Trigger on: GTEx, tissue expression, gene expression levels, expression atlas, eQTL, tissue-specific expression, TPM values.

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Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite. Use when users need to discover TF binding motifs in peaks, validate ChIP-seq targets, or find co-binding partners. Trigger on: motif analysis, HOMER, MEME, de novo motif, motif enrichment, findMotifsGenome, AME, MEME-ChIP, known motif, TF binding motif, co-factor, motif discovery.

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Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks for formal retractions, corrections, expressions of concern, and — critically — informal contradictions where subsequent studies failed to reproduce key findings. Integrates with PubMed, bioRxiv, and Consensus to provide a trust assessment. Use this skill for ANY publication evaluation, retraction checking, author reliability assessment, or when a user says "can I trust this paper", "is this study reliable", "has this been refuted", or "check this publication".

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Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.

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