Tag: regulatory-elements
Characterize Genomic Regulatory Elements Using ENCODE Data
This skill facilitates the discovery and classification of cis-regulatory elements (cCREs) by integrating ENCODE's comprehensive catalog with multi-omic data. It supports advanced analysis of chromatin states, identifying promoters, enhance…
gwas-encode integration for functional variant annotation
This skill facilitates the intersection of genome-wide association study variants with ENCODE's functional regulatory elements. It helps developers prioritise candidate causal mechanisms by identifying which disease-associated SNPs overlap …
Analyze ENCODE functional regulatory element screens
This skill facilitates the discovery and interpretation of functional regulatory elements by processing data from ENCODE's CRISPR, MPRA, and STARR-seq assays. It enables the integration of functional validation results with standard epigeno…
Comparing ENCODE data across multiple biosamples
This skill facilitates the systematic comparison of epigenomic data across diverse tissues and cell lines to distinguish constitutive regulatory elements from tissue-specific patterns. It accounts for biosample hierarchy, batch effects, and…
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.
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…
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…