スキルを探す

Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq data across donors, labs, and platforms. Follows the Mawla et al. 2019 framework for assessing cross-study reproducibility, TIN-based quality filtering, and detection-limit-aware interpretation. Handles batch correction (Harmony/Seurat), dropout awareness, cross-contamination artifacts, and platform-specific biases. Use this skill for ANY scRNA-seq integration task, cross-dataset comparison, cell atlas construction, or reproducibility assessment involving ENCODE single-cell data.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

日本語の概要は準備中です。原文の説明を表示しています。

Access ENCODE uniform analysis pipelines, generate user-specific Nextflow/WDL pipelines, manage compute resources, and integrate with cloud platforms. Use when the user wants to understand ENCODE pipelines, run pipelines on their own data, generate custom Nextflow workflows from ENCODE pipeline code, check compute requirements (CPU/GPU/memory), run pipelines in background, or integrate with Google Cloud, AWS, or other cloud platforms. Also use when the user asks about ENCODE pipeline outputs, processing standards, software versions, or wants to replicate ENCODE processing. Covers local execution, HPC, and cloud deployment with resource-aware scheduling. Use this skill for ANY pipeline execution, workflow generation, or compute resource management task involving ENCODE data.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domains, profile regulatory elements across a biosample, or understand epigenetic regulation in a specific biological context. Covers histone marks, chromatin accessibility, TF binding, transcription, DNA methylation, and 3D genome structure.

日本語の概要は準備中です。原文の説明を表示しています。

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

日本語の概要は準備中です。原文の説明を表示しています。

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal correlation, chromatin state segmentation, enhancer-gene linkage, or any analysis that requires merging or comparing data from two or more ENCODE experiments. Covers same-assay cross-sample, multi-omic same-sample, cross-organism, and perturbation integration designs. Guides compatibility checks, batch effect detection, normalization, integration strategy selection, and provenance documentation.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

日本語の概要は準備中です。原文の説明を表示しています。

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.

日本語の概要は準備中です。原文の説明を表示しています。

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

日本語の概要は準備中です。原文の説明を表示しています。

Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods, generate figure legends, create supplementary tables, draft data availability statements, compile tool citations, or auto-generate any publication text from their ENCODE analysis. Trigger on: methods section, figure legend, supplementary table, data availability, tool citations, publication writing, manuscript, write methods, methods draft, write up, write-up, paper writing, reproducible methods.

日本語の概要は準備中です。原文の説明を表示しています。

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

日本語の概要は準備中です。原文の説明を表示しています。