Tag: encode
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.
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…
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…
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…
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…