Tag: variant-annotation
Annotating Genetic Variants with ENCODE Data
Annotate genetic variants with ENCODE functional genomics data to identify causal regulatory elements and link them to target genes. The skill supports the full post-GWAS workflow, including tissue-specific mapping, enrichment testing, and …
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 …
Annotate regulatory variants with population genetics
This tool facilitates the annotation of ENCODE regulatory variants by querying gnomAD for population allele frequencies and gene constraint scores (pLI, LOEUF). It enables developers to prioritize variants by assessing rarity and functional…
Ensembl API for Variant and Gene Annotation
This tool interfaces with the Ensembl REST API to perform comprehensive genomic annotations, including variant consequence prediction (VEP), regulatory feature overlap, and coordinate liftover between assemblies. It also facilitates gene ID…
Annotating ENCODE Regulatory Variants with ClinVar
Cross-reference ENCODE functional genomic elements with ClinVar clinical variant classifications to identify pathogenic variants in regulatory regions. This skill enables both forward annotation of ENCODE peaks and reverse analysis of ClinV…
annotate non-coding variants using encode data
This skill interprets non-coding genetic variation by layering ENCODE functional genomics annotations (e.g., cCREs, enhancers) onto variant sets. It supports the full post-GWAS workflow, including tissue-specific mapping, fine-mapping, and …
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…
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…
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…
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…