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Publish Markdown to MediaWiki
Converts markdown files to wikitext and publishes them to a MediaWiki instance using the wiki CLI. The skill supports previewing changes, managing edit summaries, and applying specific themes.
Integrate multi-omics for regulatory landscape
This skill integrates diverse ENCODE datasets, including RNA-seq, ATAC-seq, and various ChIP-seq assays, to construct a comprehensive regulatory landscape. It allows users to map cell-type-specific regulatory elements by correlating gene ex…
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…
Motif discovery and enrichment analysis for peak data
Performs comprehensive de novo and known motif enrichment analysis on ChIP-seq and ATAC-seq peak data using established pipelines like HOMER and MEME Suite. This skill assists in validating target factors and identifying co-regulatory bindi…
genomic coordinate liftover workflow guide
This skill provides a definitive 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 proven…
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…
Multi-omic ENCODE Data Integration Workflow
This skill orchestrates the complex process of integrating multiple ENCODE experiments, supporting multi-omic, cross-dataset, and cross-organism analyses. It guides the user through compatibility checks, normalization strategies, and file s…
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…
Annotating GWAS Variants with ENCODE Regulatory Data
This skill facilitates the integration of GWAS Catalog variant associations with ENCODE's functional regulatory elements. It allows developers to prioritize disease-associated non-coding variants by identifying overlaps with active enhancer…
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…
Annotate regulatory variants with gnomAD data
This skill annotates ENCODE regulatory variants by querying gnomAD for population allele frequencies and gene constraint scores (LOEUF, pLI). It enables researchers to prioritise variants by assessing rarity and functional constraint, integ…
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…
Comprehensive epigenome profiling using ENCODE data
Assemble a complete epigenomic profile for any tissue or cell type by systematically gathering multiple data modalities, such as histone modifications, accessibility, and methylation, from ENCODE. The resulting profile can then be interpret…
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…
Comparing ENCODE Experiments Across Biosamples
This skill enables the systematic comparison of ENCODE experiments across various tissues, cell lines, and biosamples to identify tissue-specific regulatory patterns. It facilitates the identification of constitutive versus variable regulat…
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…
Annotate ENCODE Variants with ClinVar Data
This tool facilitates the cross-referencing of ENCODE functional genomic elements with ClinVar variant classifications. It supports both forward analysis (identifying variants within peaks) and reverse analysis (using ENCODE context to expl…
Resolving ENCODE Bulk Signals with CellxGene
This skill enables the integration of CellxGene Census single-cell RNA-seq data with bulk ENCODE functional genomics experiments to resolve cell-type-specific regulatory activity. It facilitates the deconvolution of bulk signals and the val…
Generate ENCODE Citations and Manuscript Content
This skill guides the generation of comprehensive and compliant citations for ENCODE data, covering everything from BibTeX exports to drafting data availability statements. It ensures proper attribution for manuscripts, grants, and presenta…